Variant report

Variant	rs3804627
Chromosome Location	chr3:50606374-50606375
allele	C/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	TCF12	chr3:50606166-50607404	ECC-1	luminal epithelium:	n/a	chr3:50606313-50606320
2	POLR2A	chr3:50606335-50607138	GM10847	blood:	n/a	n/a
3	HA-E2F1	chr3:50606352-50607102	MCF-7	breast:	n/a	chr3:50606885-50606892
4	BRCA1	chr3:50606219-50607110	Hela-S3	cervix:	n/a	n/a
5	MAZ	chr3:50606308-50607166	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:50606147-50607227	PFSK-1	brain:	n/a	n/a
7	TAF1	chr3:50606364-50607246	HepG2	liver:	n/a	n/a
8	TCF12	chr3:50606243-50607289	A549	lung:	n/a	chr3:50606313-50606320
9	SIN3AK20	chr3:50606281-50607199	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3A	chr3:50606246-50607343	H1-hESC	embryonic stem cell:	n/a	chr3:50606486-50606499
11	POLR2A	chr3:50606205-50607210	K562	blood:	n/a	n/a
12	POLR2A	chr3:50606334-50607115	A549	lung:	n/a	n/a
13	GABPA	chr3:50606147-50607404	MCF-7	breast:	n/a	n/a
14	ZBTB7A	chr3:50606183-50607283	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr3:50606342-50607349	Hela-S3	cervix:	n/a	n/a
16	MAX	chr3:50606320-50607272	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr3:50606321-50607257	PANC-1	pancreas:	n/a	n/a
18	NFIC	chr3:50606291-50607197	ECC-1	luminal epithelium:	n/a	n/a
19	EGR1	chr3:50606364-50607074	ECC-1	luminal epithelium:	n/a	chr3:50606975-50606990 chr3:50606520-50606542 chr3:50606605-50606615 chr3:50606605-50606616 chr3:50606522-50606536 chr3:50606605-50606615
20	TCF12	chr3:50606352-50606621	GM12878	blood:	n/a	n/a
21	IRF1	chr3:50606307-50607119	K562	blood:	n/a	chr3:50606599-50606613 chr3:50606520-50606534
22	POLR2A	chr3:50606194-50607213	U87	brain:	n/a	n/a
23	POLR2A	chr3:50606298-50606764	K562	blood:	n/a	n/a
24	CHD2	chr3:50606357-50607016	HepG2	liver:	n/a	chr3:50606885-50606892
25	TFAP2A	chr3:50606187-50607261	Hela-S3	cervix:	n/a	chr3:50606505-50606520 chr3:50606503-50606518 chr3:50606503-50606515
26	MAX	chr3:50606339-50607267	Hela-S3	cervix:	n/a	n/a
27	MTA3	chr3:50606153-50607337	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:50606292-50607282	GM18505	blood:	n/a	n/a
29	POLR2A	chr3:50606357-50607284	H1-hESC	embryonic stem cell:	n/a	n/a
30	SP1	chr3:50606315-50607075	HepG2	liver:	n/a	chr3:50606573-50606583 chr3:50606523-50606533 chr3:50606523-50606533 chr3:50606523-50606532 chr3:50606573-50606583 chr3:50606601-50606613 chr3:50606981-50606991 chr3:50606601-50606613 chr3:50606981-50606991
31	POLR2A	chr3:50606256-50607317	HUVEC	blood vessel:	n/a	n/a
32	GABPA	chr3:50606354-50607140	HepG2	liver:	n/a	n/a
33	ELF1	chr3:50606269-50607204	SK-N-SH	brain:	n/a	chr3:50606897-50606906 chr3:50606895-50606906 chr3:50606895-50606906
34	BHLHE40	chr3:50606315-50606995	K562	blood:	n/a	n/a
35	PBX3	chr3:50606269-50607257	SK-N-SH	brain:	n/a	n/a
36	TBP	chr3:50606249-50607305	K562	blood:	n/a	n/a
37	TCF12	chr3:50606328-50607060	GM12878	blood:	n/a	n/a
38	GABPA	chr3:50606357-50607338	SK-N-SH	brain:	n/a	n/a
39	GABPA	chr3:50606369-50607162	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:50606306-50607263	HUVEC	blood vessel:	n/a	n/a
41	CTCF	chr3:50606345-50606523	K562	blood:	n/a	chr3:50606395-50606404
42	KAP1	chr3:50606318-50607012	U2OS	brain:	n/a	n/a
43	POLR2A	chr3:50606328-50607177	HepG2	liver:	n/a	n/a
44	YY1	chr3:50606340-50607061	SK-N-SH_RA	brain:	n/a	n/a
45	TAL1	chr3:50606342-50607068	K562	blood:	n/a	chr3:50606532-50606547 chr3:50606533-50606544 chr3:50606532-50606547 chr3:50606532-50606547
46	POLR2A	chr3:50606274-50607233	K562	blood:	n/a	n/a
47	GABPA	chr3:50606241-50607357	A549	lung:	n/a	n/a
48	POLR2A	chr3:50606362-50606702	A549	lung:	n/a	n/a
49	NFIC	chr3:50606286-50607219	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr3:50606282-50607206	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:50606346-50606396	ovcar-3	ovarian:	n/a
2	chr3:50606346-50606396	A549	lung:	n/a
3	chr3:50606346-50606396	HNPCEpiC	eye:	n/a
4	chr3:50606346-50606396	AG10803	skin:	n/a
5	chr3:50606346-50606396	PFSK-1	brain:	n/a
6	chr3:50606346-50606396	HEEpiC	esophagus:	n/a
7	chr3:50606346-50606396	HCT-116	colon:	n/a
8	chr3:50606346-50606396	ProgFib	skin:	n/a
9	chr3:50606346-50606396	BE2_C	brain:	n/a
10	chr3:50606346-50606396	MCF-7	breast:	n/a
11	chr3:50606346-50606396	NT2-D1	testis:	n/a
12	chr3:50606346-50606396	Caco-2	colon:	n/a
13	chr3:50606346-50606396	HCF	heart:	n/a
14	chr3:50606346-50606396	HRCEpiC	kidney:	n/a
15	chr3:50606346-50606396	SK-N-SH_RA	brain:	n/a
16	chr3:50606346-50606396	IMR90	lung:	fetal
17	chr3:50606346-50606396	AG04449	skin:	fetal
18	chr3:50606346-50606396	GM06990	blood:	n/a
19	chr3:50606346-50606396	SKMC	muscle:	n/a
20	chr3:50606346-50606396	HepG2	liver:	n/a
21	chr3:50606346-50606396	SAEC	small airway:	n/a
22	chr3:50606346-50606396	HUVEC	blood vessel:	n/a
23	chr3:50606346-50606396	PrEC	prostate:	n/a
24	chr3:50606346-50606396	AG09309	skin:	n/a
25	chr3:50606346-50606396	HIPEpiC	eye:	n/a
26	chr3:50606346-50606396	GM12891	blood:	n/a
27	chr3:50606346-50606396	Hela-S3	cervix:	n/a
28	chr3:50606346-50606396	NHDF-neo	bronchial:	n/a
29	chr3:50606346-50606396	HPAEpiC	pulmonary alveolar:	n/a
30	chr3:50606346-50606396	NHBE	bronchial:	n/a
31	chr3:50606346-50606396	HL-60	blood:	n/a
32	chr3:50606346-50606396	AoSMC	blood vessel:	n/a
33	chr3:50606346-50606396	GM19239	blood:	n/a
34	chr3:50606346-50606396	AG04450	lung:	fetal
35	chr3:50606346-50606396	SK-N-SH	brain:	n/a
36	chr3:50606346-50606396	CMK	blood:	n/a
37	chr3:50606346-50606396	HAEpiC	amniotic membrane:	n/a
38	chr3:50606346-50606396	Jurkat	blood:	n/a
39	chr3:50606346-50606396	BJ	skin:	n/a
40	chr3:50606346-50606396	T-47D	breast:	n/a
41	chr3:50606346-50606396	ECC-1	luminal epithelium:	n/a
42	chr3:50606346-50606396	U87	brain:	n/a
43	chr3:50606346-50606396	AG09319	gingival:	n/a
44	chr3:50606346-50606396	HRE	kidney:	n/a
45	chr3:50606346-50606396	HCM	heart:	n/a
46	chr3:50606346-50606396	GM12892	blood:	n/a
47	chr3:50606346-50606396	HMEC	breast:	n/a
48	chr3:50606346-50606396	Hepatocyte	liver:	n/a
49	chr3:50606346-50606396	H1-hESC	embryonic stem cell:	embryo
50	chr3:50606346-50606396	LNCaP	prostate:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50605679..50607694-chr6:90346835..90349653,2	MCF-7	breast:
2	chr3:50603678..50606532-chr3:50606738..50608762,2	K562	blood:
3	chr3:50402920..50405878-chr3:50604369..50606579,2	K562	blood:
4	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
5	chr3:50601756..50613871-chr3:50647072..50654542,28	K562	blood:
6	chr3:50603678..50606671-chr3:50607262..50609999,2	K562	blood:

Variant related genes	Relation type
C3orf18	TF binding region
HEMK1	TF binding region
C3orf18	CpG island
HEMK1	CpG island
ENSG00000114735	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000007402	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000083099	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000271858	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1013233	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1034405	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs11130252	0.84[EUR][1000 genomes]
rs11712367	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap]
rs11716398	0.82[AMR][1000 genomes]
rs11719998	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12491425	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12493985	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12639126	0.80[CEU][hapmap]
rs129310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13076850	0.89[EUR][1000 genomes]
rs13083004	0.89[EUR][1000 genomes]
rs13084476	0.84[EUR][1000 genomes]
rs13091933	0.94[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs13094336	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1385025	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs175634	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17787569	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1824281	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs1971976	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs201193	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs201194	0.94[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs201196	0.91[EUR][1000 genomes]
rs201197	0.80[EUR][1000 genomes]
rs201198	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2170840	0.95[LWK][hapmap];0.87[MKK][hapmap]
rs2227280	0.90[EUR][1000 genomes]
rs2232248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2232253	0.90[EUR][1000 genomes]
rs2269505	0.94[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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2269507	0.90[EUR][1000 genomes]
rs2355321	0.90[EUR][1000 genomes]
rs2355323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2608988	0.86[TSI][hapmap]
rs2609024	0.86[TSI][hapmap]
rs2675773	0.87[CEU][hapmap]
rs2675810	0.86[TSI][hapmap]
rs34202063	0.90[EUR][1000 genomes]
rs34267788	0.81[EUR][1000 genomes]
rs34399912	0.90[EUR][1000 genomes]
rs34434811	0.81[EUR][1000 genomes]
rs34584636	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs34756253	0.84[EUR][1000 genomes]
rs34848480	0.84[AMR][1000 genomes]
rs34889917	0.90[EUR][1000 genomes]
rs35655236	0.89[EUR][1000 genomes]
rs35690191	0.89[EUR][1000 genomes]
rs35714264	0.85[EUR][1000 genomes]
rs35864641	0.81[EUR][1000 genomes]
rs375544	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3792325	0.90[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3792328	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3804632	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs388483	0.93[YRI][hapmap]
rs391620	0.94[EUR][1000 genomes]
rs3943212	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs396302	0.94[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs398703	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs399484	1.00[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs399971	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs414171	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs417592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs441516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs443030	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs443436	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs448028	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4485709	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs4533647	0.81[EUR][1000 genomes]
rs453570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688712	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs490634	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs59949730	0.90[EUR][1000 genomes]
rs616589	0.90[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs616689	0.96[LWK][hapmap];0.87[MKK][hapmap]
rs622502	0.81[EUR][1000 genomes]
rs628081	0.94[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6446212	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs6446213	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap]
rs67588094	0.90[EUR][1000 genomes]
rs6778680	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs6779819	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes]
rs67813889	0.92[EUR][1000 genomes]
rs6784166	0.85[EUR][1000 genomes]
rs6787521	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6791880	0.86[TSI][hapmap]
rs6796769	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap]
rs695170	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71326937	0.90[EUR][1000 genomes]
rs728901	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs750453	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs750510	0.82[ASW][hapmap];0.89[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs751851	0.84[AMR][1000 genomes]
rs754298	0.81[CHD][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs7615703	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs7635666	0.82[AMR][1000 genomes]
rs7646236	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs808149	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs809451	0.81[EUR][1000 genomes]
rs809454	0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs813243	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs876104	0.96[LWK][hapmap];0.87[MKK][hapmap]
rs900735	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9682401	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9825535	0.88[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs9826757	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9830920	0.82[EUR][1000 genomes]
rs9879397	0.96[LWK][hapmap];0.86[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3804627	HEMK1	cis	parietal	SCAN
rs3804627	HEMK1	cis	cerebellum	SCAN
rs3804627	ALS2CL	cis	parietal	SCAN
rs3804627	MST1	cis	cerebellum	SCAN
rs3804627	APEH	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50604000-50606400	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr3:50604200-50606400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr3:50604200-50606600	Flanking Active TSS	Dnd41	blood
4	chr3:50604200-50608400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:50604400-50606800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:50604400-50607600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr3:50604400-50607600	Active TSS	Fetal Kidney	kidney
8	chr3:50604400-50608000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:50604600-50606400	Flanking Active TSS	Primary B cells from peripheral blood	blood
10	chr3:50604600-50606600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr3:50604600-50607600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:50604600-50607600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:50604600-50607800	Active TSS	Aorta	Aorta
14	chr3:50604600-50607800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr3:50604600-50607800	Active TSS	Psoas Muscle	Psoas
16	chr3:50604600-50608000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:50604600-50608000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:50604800-50606400	Enhancers	Fetal Brain Male	brain
19	chr3:50604800-50607400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:50604800-50607600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:50604800-50607600	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr3:50604800-50607600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:50604800-50607600	Active TSS	Esophagus	oesophagus
24	chr3:50604800-50607600	Active TSS	HSMMtube	muscle
25	chr3:50604800-50607800	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr3:50604800-50607800	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr3:50604800-50607800	Active TSS	Ovary	ovary
28	chr3:50605000-50607400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:50605000-50607600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:50605000-50607600	Active TSS	HSMM	muscle
31	chr3:50605000-50607800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:50605000-50607800	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr3:50605000-50608000	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr3:50605000-50608200	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr3:50605000-50608200	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr3:50605200-50606400	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr3:50605200-50606600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr3:50605200-50606600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:50605200-50606600	Enhancers	Spleen	Spleen
40	chr3:50605200-50607600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr3:50605200-50607800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr3:50605400-50606400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:50605600-50606400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:50605600-50607600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:50605600-50607600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:50605600-50607600	Active TSS	Thymus	Thymus
47	chr3:50605600-50607800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:50605600-50608200	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr3:50605800-50607000	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr3:50605800-50607000	Active TSS	Colonic Mucosa	Colon

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