Variant report

Variant	rs3809540
Chromosome Location	chr15:55489412-55489413
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr15:55488789-55489419	GM12878	blood:	n/a	chr15:55489131-55489138 chr15:55489128-55489141
2	CTCF	chr15:55489173-55489475	GM12878	blood:	n/a	chr15:55489339-55489360 chr15:55489344-55489362 chr15:55489345-55489361
3	GABPA	chr15:55488606-55489602	MCF-7	breast:	n/a	chr15:55488843-55488850 chr15:55489285-55489299
4	CEBPB	chr15:55488155-55489674	Hela-S3	cervix:	n/a	chr15:55489137-55489148 chr15:55488577-55488590
5	CREB1	chr15:55488819-55489635	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr15:55488598-55489528	H1-hESC	embryonic stem cell:	n/a	n/a
7	TBL1XR1	chr15:55488629-55489604	K562	blood:	n/a	n/a
8	POLR2A	chr15:55488329-55489664	HL-60	blood:	n/a	n/a
9	POLR2A	chr15:55488517-55489789	K562	blood:	n/a	n/a
10	CTCF	chr15:55489300-55489450	HCM	heart:	n/a	chr15:55489339-55489360 chr15:55489344-55489362 chr15:55489345-55489361
11	RFX5	chr15:55488876-55489550	K562	blood:	n/a	n/a
12	EP300	chr15:55488919-55489781	GM12878	blood:	n/a	chr15:55489155-55489162 chr15:55488937-55488953 chr15:55489134-55489148
13	POLR2A	chr15:55488887-55489631	ECC-1	luminal epithelium:	n/a	n/a
14	HEY1	chr15:55488797-55489569	HepG2	liver:	n/a	n/a
15	CTCF	chr15:55489320-55489470	HAc	cerebellar:	n/a	chr15:55489339-55489360 chr15:55489344-55489362 chr15:55489345-55489361
16	ATF1	chr15:55488973-55489508	K562	blood:	n/a	n/a
17	SIX5	chr15:55488810-55489709	A549	lung:	n/a	chr15:55489330-55489344
18	SPI1	chr15:55488931-55489437	GM12891	blood:	n/a	chr15:55489131-55489138 chr15:55489128-55489141
19	REST	chr15:55488557-55489626	A549	lung:	n/a	n/a
20	YY1	chr15:55488982-55489447	HCT-116	colon:	n/a	n/a
21	POLR2A	chr15:55488769-55489560	A549	lung:	n/a	n/a
22	CTCF	chr15:55488647-55489655	GM12878	blood:	n/a	chr15:55489339-55489360 chr15:55489344-55489362 chr15:55489345-55489361
23	NRF1	chr15:55489069-55489520	GM12878	blood:	n/a	chr15:55489285-55489299 chr15:55489285-55489296
24	ATF3	chr15:55488694-55489633	A549	lung:	n/a	chr15:55488948-55488957
25	HCFC1	chr15:55488672-55489830	K562	blood:	n/a	n/a
26	CTCF	chr15:55489139-55489573	GM19238	blood:	n/a	chr15:55489339-55489360 chr15:55489344-55489362 chr15:55489345-55489361
27	HA-E2F1	chr15:55488637-55489685	MCF-7	breast:	n/a	chr15:55489286-55489295
28	CTCF	chr15:55489171-55489491	MCF-7	breast:	n/a	chr15:55489339-55489360 chr15:55489344-55489362 chr15:55489345-55489361
29	POLR2A	chr15:55488739-55489564	GM12878	blood:	n/a	n/a
30	MAX	chr15:55488612-55489668	ECC-1	luminal epithelium:	n/a	n/a
31	MAX	chr15:55488638-55489576	K562	blood:	n/a	n/a
32	POLR2A	chr15:55488423-55489521	HUVEC	blood vessel:	n/a	n/a
33	CTCF	chr15:55489139-55489432	GM12891	blood:	n/a	chr15:55489339-55489360 chr15:55489344-55489362 chr15:55489345-55489361
34	POLR2A	chr15:55488692-55489668	GM15510	blood:	n/a	n/a
35	GABPA	chr15:55488637-55489533	K562	blood:	n/a	chr15:55488843-55488850 chr15:55489285-55489299
36	CTCF	chr15:55489135-55489527	MCF-7	breast:	n/a	chr15:55489339-55489360 chr15:55489344-55489362 chr15:55489345-55489361
37	POLR2A	chr15:55488354-55489645	Hela-S3	cervix:	n/a	n/a
38	MBD4	chr15:55488858-55489415	HepG2	liver:	n/a	n/a
39	MAX	chr15:55488613-55489582	H1-hESC	embryonic stem cell:	n/a	n/a
40	EP300	chr15:55488887-55489830	GM12878	blood:	n/a	chr15:55489155-55489162 chr15:55488937-55488953 chr15:55489134-55489148
41	POLR2A	chr15:55487585-55489837	MCF10A-Er-Src	breast:	n/a	n/a
42	YY1	chr15:55489010-55489481	SK-N-SH_RA	brain:	n/a	n/a
43	CTCF	chr15:55489280-55489430	A549	lung:	n/a	chr15:55489339-55489360 chr15:55489344-55489362 chr15:55489345-55489361
44	POLR2A	chr15:55488429-55489608	SK-N-MC	brain:	n/a	n/a
45	POLR2A	chr15:55486370-55489557	K562	blood:	n/a	n/a
46	POLR2A	chr15:55488856-55489990	HCT-116	colon:	n/a	n/a
47	RUNX3	chr15:55488726-55489830	GM12878	blood:	n/a	n/a
48	TAF1	chr15:55488720-55489486	HepG2	liver:	n/a	n/a
49	MAX	chr15:55488649-55489595	MCF-7	breast:	n/a	n/a
50	ELF1	chr15:55488688-55489522	GM12878	blood:	n/a	chr15:55489127-55489140

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:55489399-55489449	PrEC	prostate:	n/a
2	chr15:55489399-55489449	GM19239	blood:	n/a
3	chr15:55489399-55489449	LNCaP	prostate:	n/a
4	chr15:55489374-55489424	Jurkat	blood:	n/a
5	chr15:55489399-55489449	HRPEpiC	eye:	n/a
6	chr15:55489399-55489449	HCPEpiC	choroid plexus:	n/a
7	chr15:55489374-55489424	HEEpiC	esophagus:	n/a
8	chr15:55489374-55489424	AG10803	skin:	n/a
9	chr15:55489374-55489424	HPAEpiC	pulmonary alveolar:	n/a
10	chr15:55489374-55489424	NB4	blood:	n/a
11	chr15:55489374-55489424	Hela-S3	cervix:	n/a
12	chr15:55489374-55489424	NHDF-neo	bronchial:	n/a
13	chr15:55489399-55489449	NB4	blood:	n/a
14	chr15:55489399-55489449	HEK293	kidney:	embryo
15	chr15:55489399-55489449	NT2-D1	testis:	n/a
16	chr15:55489374-55489424	T-47D	breast:	n/a
17	chr15:55489374-55489424	BJ	skin:	n/a
18	chr15:55489374-55489424	SAEC	small airway:	n/a
19	chr15:55489399-55489449	HRE	kidney:	n/a
20	chr15:55489374-55489424	HIPEpiC	eye:	n/a
21	chr15:55489374-55489424	H1-hESC	embryonic stem cell:	embryo
22	chr15:55489374-55489424	GM12892	blood:	n/a
23	chr15:55489399-55489449	K562	blood:	n/a
24	chr15:55489374-55489424	HUVEC	blood vessel:	n/a
25	chr15:55489399-55489449	AG09319	gingival:	n/a
26	chr15:55489399-55489449	NHBE	bronchial:	n/a
27	chr15:55489399-55489449	H1-hESC	embryonic stem cell:	embryo
28	chr15:55489374-55489424	Caco-2	colon:	n/a
29	chr15:55489399-55489449	AoSMC	blood vessel:	n/a
30	chr15:55489399-55489449	Hela-S3	cervix:	n/a
31	chr15:55489399-55489449	ECC-1	luminal epithelium:	n/a
32	chr15:55489374-55489424	HCM	heart:	n/a
33	chr15:55489399-55489449	AG04450	lung:	fetal
34	chr15:55489399-55489449	HIPEpiC	eye:	n/a
35	chr15:55489399-55489449	T-47D	breast:	n/a
36	chr15:55489399-55489449	HCF	heart:	n/a
37	chr15:55489374-55489424	LNCaP	prostate:	n/a
38	chr15:55489374-55489424	AG04449	skin:	fetal
39	chr15:55489374-55489424	PANC-1	pancreas:	n/a
40	chr15:55489374-55489424	HEK293	kidney:	embryo
41	chr15:55489374-55489424	AG04450	lung:	fetal
42	chr15:55489399-55489449	RPTEC	kidney:	n/a
43	chr15:55489399-55489449	HEEpiC	esophagus:	n/a
44	chr15:55489399-55489449	CMK	blood:	n/a
45	chr15:55489399-55489449	GM06990	blood:	n/a
46	chr15:55489399-55489449	HPAEpiC	pulmonary alveolar:	n/a
47	chr15:55489374-55489424	ProgFib	skin:	n/a
48	chr15:55489374-55489424	HMEC	breast:	n/a
49	chr15:55489399-55489449	Hepatocyte	liver:	n/a
50	chr15:55489399-55489449	SK-N-MC	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:55484699..55490442-chr15:55579270..55584640,8	K562	blood:
2	chr15:55489042..55491644-chr15:55640711..55643190,2	K562	blood:
3	chr15:55488451..55490602-chr15:55640573..55642962,2	MCF-7	breast:
4	chr15:55485508..55492313-chr15:55579801..55583590,12	K562	blood:
5	chr15:55488699..55489437-chr3:49710788..49711819,3	Hela-S3	cervix:
6	chr15:55488902..55489642-chr19:33793325..33793871,2	HCT-116	colon:
7	chr15:55489108..55489798-chr16:89626508..89627135,2	NB4	blood:
8	chr15:54266407..54270072-chr15:55486535..55491034,4	MCF-7	breast:
9	chr15:55488918..55489744-chr9:128003531..128004033,2	Hela-S3	cervix:
10	chr11:62608973..62609631-chr15:55489207..55489789,2	Hela-S3	cervix:

Variant related genes	Relation type
RSL24D1	TF binding region
RSL24D1	CpG island
ENSG00000230259	Chromatin interaction
ENSG00000239705	Chromatin interaction
ENSG00000069974	Chromatin interaction
ENSG00000260916	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000167526	Chromatin interaction
ENSG00000267296	Chromatin interaction
ENSG00000044574	Chromatin interaction
ENSG00000069943	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000259669	Chromatin interaction
ENSG00000245848	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10162819	0.90[ASN][1000 genomes]
rs10162843	0.90[ASN][1000 genomes]
rs1050931	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10518804	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1061821	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061822	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1061823	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1061824	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1061870	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1061873	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1061874	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061875	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11852763	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11855907	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11855973	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11855978	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11856010	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11857087	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12385963	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12440420	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs13380400	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976036	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs16976039	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs16976065	0.85[ASN][1000 genomes]
rs16976083	0.85[ASN][1000 genomes]
rs16976094	0.89[ASN][1000 genomes]
rs16976116	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16976149	0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs16976177	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs17238171	1.00[JPT][hapmap]
rs28433503	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28449712	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28489312	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28499113	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28508034	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28522816	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28526269	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28530662	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28535372	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28541469	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28558576	0.89[ASN][1000 genomes]
rs28562431	0.90[ASN][1000 genomes]
rs28564077	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28589384	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28589609	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28590021	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28591259	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28592928	0.84[ASN][1000 genomes]
rs28600759	0.81[ASN][1000 genomes]
rs28630909	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28636526	0.88[ASN][1000 genomes]
rs28649719	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28673043	0.85[ASN][1000 genomes]
rs28699327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28704109	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28706531	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28708989	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28710976	0.97[ASN][1000 genomes]
rs28714578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28784096	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28864456	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28889339	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2899580	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899581	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899582	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3179664	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759861	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809539	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4238316	0.89[ASN][1000 genomes]
rs4503734	0.96[ASN][1000 genomes]
rs4545742	0.88[ASN][1000 genomes]
rs4632077	1.00[JPT][hapmap]
rs56328329	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62020097	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62020114	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493767	0.87[CHB][hapmap]
rs6493768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493769	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493771	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7165491	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7168472	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs7168737	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172108	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172289	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176676	0.85[ASN][1000 genomes]
rs7179365	0.90[ASN][1000 genomes]
rs7180594	0.90[ASN][1000 genomes]
rs7181237	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7183255	1.00[JPT][hapmap]
rs73409851	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73409853	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8027098	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8027256	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8028525	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8030981	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8031949	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8033588	0.92[CHB][hapmap];0.90[ASN][1000 genomes]
rs8034063	0.90[ASN][1000 genomes]
rs8034402	1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[ASN][1000 genomes]
rs8034853	0.90[ASN][1000 genomes]
rs8034882	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs8035625	1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[ASN][1000 genomes]
rs8043029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920136	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9920219	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9920220	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9920737	0.89[CEU][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3809540	TMEM30B	trans	brain	seeQTL
rs3809540	C15orf15	cis	multi-tissue	Pritchard
rs3809540	GJB2	trans	brain	seeQTL
rs3809540	TNFRSF11B	trans	brain	seeQTL
rs3809540	RSL24D1	cis	parietal	SCAN
rs3809540	PIGB	cis	Artery Tibial	GTEx
rs3809540	RAB27A	Cis_1M	lymphoblastoid	RTeQTL
rs3809540	SSTR2	trans	brain	seeQTL
rs3809540	C2orf40	trans	brain	seeQTL
rs3809540	RAB27A	cis	multi-tissue	Pritchard
rs3809540	RSL24D1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55485600-55490600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:55486600-55490000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:55486800-55490000	Active TSS	Psoas Muscle	Psoas
4	chr15:55487000-55489800	Active TSS	Colonic Mucosa	Colon
5	chr15:55487000-55490000	Active TSS	NHLF	lung
6	chr15:55487200-55490000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:55487200-55490200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr15:55487400-55489600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:55487400-55490000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr15:55487400-55490200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr15:55487400-55490200	Active TSS	Right Atrium	heart
12	chr15:55487600-55490000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:55487600-55490000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:55487600-55490000	Active TSS	Fetal Brain Female	brain
15	chr15:55487600-55490200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:55487600-55490400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr15:55487800-55489800	Active TSS	Placenta Amnion	Placenta Amnion
18	chr15:55487800-55490000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:55487800-55490000	Active TSS	H9 Cell Line	embryonic stem cell
20	chr15:55487800-55490000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:55487800-55490000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:55487800-55490000	Active TSS	Fetal Intestine Small	intestine
23	chr15:55487800-55490000	Active TSS	Ovary	ovary
24	chr15:55487800-55490000	Active TSS	HSMMtube	muscle
25	chr15:55487800-55490200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:55487800-55490200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr15:55487800-55490200	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr15:55487800-55490200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:55487800-55490200	Active TSS	Right Ventricle	heart
30	chr15:55487800-55490400	Active TSS	K562	blood
31	chr15:55488000-55489600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:55488000-55489600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:55488000-55489600	Bivalent/Poised TSS	HepG2	liver
34	chr15:55488000-55489800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:55488000-55489800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:55488000-55489800	Active TSS	Muscle Satellite Cultured Cells	--
37	chr15:55488000-55489800	Active TSS	Colon Smooth Muscle	Colon
38	chr15:55488000-55489800	Active TSS	Fetal Thymus	thymus
39	chr15:55488000-55489800	Active TSS	Small Intestine	intestine
40	chr15:55488000-55489800	Active TSS	NHDF-Ad	bronchial
41	chr15:55488000-55490000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr15:55488000-55490000	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr15:55488000-55490000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:55488000-55490000	Active TSS	Primary T cells fromperipheralblood	blood
45	chr15:55488000-55490000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:55488000-55490000	Active TSS	Brain Anterior Caudate	brain
47	chr15:55488000-55490000	Active TSS	Fetal Intestine Large	intestine
48	chr15:55488000-55490000	Active TSS	Fetal Muscle Trunk	muscle
49	chr15:55488000-55490000	Active TSS	Left Ventricle	heart
50	chr15:55488000-55490000	Active TSS	HSMM	muscle

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