Variant report

Variant	rs7631704
Chromosome Location	chr3:143690416-143690417
allele	A/G
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	CTCF	chr3:143690320-143690610	BJ	skin:	n/a	n/a
2	ZBTB7A	chr3:143689675-143691051	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr3:143690378-143691111	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:143689636-143692179	H1-hESC	embryonic stem cell:	n/a	n/a
5	HDAC2	chr3:143689898-143692374	MCF-7	breast:	n/a	chr3:143690819-143690828 chr3:143690369-143690383
6	POLR2A	chr3:143689448-143692708	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:143689953-143692471	GM12891	blood:	n/a	n/a
8	POLR2A	chr3:143689718-143692074	HEK293	kidney:	n/a	n/a
9	BACH1	chr3:143690053-143691021	H1-hESC	embryonic stem cell:	n/a	n/a
10	REST	chr3:143689428-143691555	H1-neurons	neurons:	n/a	chr3:143689885-143689905 chr3:143689912-143689925
11	TCF12	chr3:143690111-143691224	ECC-1	luminal epithelium:	n/a	n/a
12	EGR1	chr3:143690104-143690739	GM12878	blood:	n/a	chr3:143690541-143690554 chr3:143690619-143690629 chr3:143690625-143690635 chr3:143690540-143690555 chr3:143690541-143690554 chr3:143690621-143690634
13	IRF1	chr3:143690011-143691085	K562	blood:	n/a	chr3:143690567-143690584 chr3:143690412-143690429 chr3:143690250-143690264 chr3:143690616-143690630 chr3:143690412-143690424 chr3:143690602-143690616 chr3:143690483-143690494 chr3:143690180-143690194
14	TCF7L2	chr3:143689631-143692487	HCT-116	colon:	n/a	n/a
15	BRCA1	chr3:143689916-143691085	Hela-S3	cervix:	n/a	n/a
16	MAX	chr3:143689475-143692453	A549	lung:	n/a	chr3:143689817-143689826 chr3:143689829-143689838 chr3:143689513-143689522
17	NFIC	chr3:143689875-143690940	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:143689516-143692415	HL-60	blood:	n/a	n/a
19	MAX	chr3:143689667-143692276	ECC-1	luminal epithelium:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
20	BRCA1	chr3:143690389-143690910	GM12878	blood:	n/a	n/a
21	MYC	chr3:143689557-143692334	K562	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
22	SRF	chr3:143689944-143691057	ECC-1	luminal epithelium:	n/a	chr3:143690277-143690292 chr3:143690276-143690294 chr3:143690274-143690292 chr3:143690280-143690294 chr3:143690278-143690291 chr3:143690278-143690289 chr3:143690280-143690289 chr3:143690276-143690290 chr3:143690279-143690296 chr3:143690276-143690293 chr3:143690279-143690290
23	POLR2A	chr3:143689882-143692298	MCF-7	breast:	n/a	n/a
24	CTCF	chr3:143690340-143690490	HPF	lung:	n/a	n/a
25	FOXM1	chr3:143689578-143692479	GM12878	blood:	n/a	n/a
26	STAT5A	chr3:143690235-143691133	GM12878	blood:	n/a	chr3:143690864-143690876 chr3:143690358-143690365 chr3:143690860-143690872
27	POLR2A	chr3:143689635-143692573	GM12878	blood:	n/a	n/a
28	CEBPB	chr3:143690163-143690586	IMR90	lung:	n/a	n/a
29	NFIC	chr3:143690125-143691170	ECC-1	luminal epithelium:	n/a	n/a
30	MAX	chr3:143689459-143692886	Hela-S3	cervix:	n/a	chr3:143689817-143689826 chr3:143689829-143689838 chr3:143689513-143689522
31	POLR2A	chr3:143689651-143692557	GM18526	blood:	n/a	n/a
32	MYC	chr3:143689633-143692296	K562	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
33	CTCF	chr3:143690280-143690430	HEEpiC	esophagus:	n/a	n/a
34	MAX	chr3:143689528-143692416	HCT-116	colon:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
35	ETS1	chr3:143690251-143691114	A549	lung:	n/a	chr3:143690359-143690366 chr3:143690620-143690631
36	POLR2A	chr3:143689924-143691808	A549	lung:	n/a	n/a
37	CTCF	chr3:143689842-143690495	K562	blood:	n/a	n/a
38	POLR2A	chr3:143689670-143692495	GM15510	blood:	n/a	n/a
39	CUX1	chr3:143689941-143690461	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:143689852-143691849	GM12878	blood:	n/a	n/a
41	MXI1	chr3:143689654-143692425	GM12878	blood:	n/a	chr3:143689823-143689838 chr3:143689811-143689826
42	MAX	chr3:143689675-143691869	A549	lung:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
43	POLR2A	chr3:143689898-143692254	MCF-7	breast:	n/a	n/a
44	ELF1	chr3:143690006-143691105	MCF-7	breast:	n/a	chr3:143691041-143691053 chr3:143690785-143690797
45	RUNX3	chr3:143689706-143692538	GM12878	blood:	n/a	chr3:143690436-143690445 chr3:143690436-143690445 chr3:143690482-143690497
46	CTCF	chr3:143690300-143690450	HMF	breast:	n/a	n/a
47	CREB1	chr3:143689619-143691129	H1-hESC	embryonic stem cell:	n/a	n/a
48	MXI1	chr3:143689589-143692923	Hela-S3	cervix:	n/a	chr3:143689823-143689838 chr3:143689811-143689826 chr3:143689595-143689604
49	MYC	chr3:143689554-143692333	NB4	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
50	SIN3AK20	chr3:143689603-143691944	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:143690404-143690454	ProgFib	skin:	n/a
2	chr3:143690404-143690454	HRPEpiC	eye:	n/a
3	chr3:143690404-143690454	CMK	blood:	n/a
4	chr3:143690404-143690454	HCM	heart:	n/a
5	chr3:143690404-143690454	A549	lung:	n/a
6	chr3:143690404-143690454	HCT-116	colon:	n/a
7	chr3:143690404-143690454	NHBE	bronchial:	n/a
8	chr3:143690404-143690454	MCF-7	breast:	n/a
9	chr3:143690404-143690454	HL-60	blood:	n/a
10	chr3:143690404-143690454	ECC-1	luminal epithelium:	n/a
11	chr3:143690404-143690454	HCPEpiC	choroid plexus:	n/a
12	chr3:143690404-143690454	GM19239	blood:	n/a
13	chr3:143690404-143690454	NB4	blood:	n/a
14	chr3:143690404-143690454	AoSMC	blood vessel:	n/a
15	chr3:143690404-143690454	Jurkat	blood:	n/a
16	chr3:143690404-143690454	NH-A	brain:	n/a
17	chr3:143690404-143690454	HNPCEpiC	eye:	n/a
18	chr3:143690404-143690454	GM12891	blood:	n/a
19	chr3:143690404-143690454	HAEpiC	amniotic membrane:	n/a
20	chr3:143690404-143690454	AG10803	skin:	n/a
21	chr3:143690404-143690454	LNCaP	prostate:	n/a
22	chr3:143690404-143690454	HRCEpiC	kidney:	n/a
23	chr3:143690404-143690454	HUVEC	blood vessel:	n/a
24	chr3:143690404-143690454	SKMC	muscle:	n/a
25	chr3:143690404-143690454	HepG2	liver:	n/a
26	chr3:143690404-143690454	U87	brain:	n/a
27	chr3:143690404-143690454	GM12878	blood:	n/a
28	chr3:143690404-143690454	MCF10A-Er-Src	breast:	n/a
29	chr3:143690404-143690454	GM06990	blood:	n/a
30	chr3:143690404-143690454	HRE	kidney:	n/a
31	chr3:143690404-143690454	AG04450	lung:	fetal
32	chr3:143690404-143690454	Caco-2	colon:	n/a
33	chr3:143690404-143690454	Hela-S3	cervix:	n/a
34	chr3:143690404-143690454	SK-N-SH_RA	brain:	n/a
35	chr3:143690404-143690454	PrEC	prostate:	n/a
36	chr3:143690404-143690454	BE2_C	brain:	n/a
37	chr3:143690404-143690454	SK-N-MC	brain:	n/a
38	chr3:143690404-143690454	H1-hESC	embryonic stem cell:	embryo
39	chr3:143690404-143690454	IMR90	lung:	fetal
40	chr3:143690404-143690454	SK-N-SH	brain:	n/a
41	chr3:143690404-143690454	AG09319	gingival:	n/a
42	chr3:143690404-143690454	ovcar-3	ovarian:	n/a
43	chr3:143690404-143690454	HEEpiC	esophagus:	n/a
44	chr3:143690404-143690454	HCF	heart:	n/a
45	chr3:143690404-143690454	AG09309	skin:	n/a
46	chr3:143690404-143690454	BJ	skin:	n/a
47	chr3:143690404-143690454	RPTEC	kidney:	n/a
48	chr3:143690404-143690454	AG04449	skin:	fetal
49	chr3:143690404-143690454	SAEC	small airway:	n/a
50	chr3:143690404-143690454	NHDF-neo	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:25621104..25621916-chr3:143690294..143691222,2	Hela-S3	cervix:
2	chr3:143689958..143690542-chr6:44224790..44225315,2	Hela-S3	cervix:
3	chr10:98592013..98592977-chr3:143690256..143690764,2	Hela-S3	cervix:
4	chr22:19418740..19420583-chr3:143689830..143691587,2	MCF-7	breast:
5	chr11:17097769..17100478-chr3:143690055..143692307,2	MCF-7	breast:
6	chr19:44258720..44259380-chr3:143690069..143691057,2	Hela-S3	cervix:
7	chr12:12956339..12957122-chr3:143689535..143690489,2	Hela-S3	cervix:
8	chr3:143688929..143690453-chr9:116724811..116727064,2	MCF-7	breast:
9	chr12:16064190..16064741-chr3:143690280..143690998,2	Hela-S3	cervix:
10	chr12:92539191..92539985-chr3:143690264..143691024,2	Hela-S3	cervix:
11	chr17:57914617..57916585-chr3:143689584..143691332,2	MCF-7	breast:
12	chr3:143689777..143690496-chr6:26055384..26056279,2	Hela-S3	cervix:
13	chr19:18682649..18683371-chr3:143690264..143691172,2	Hela-S3	cervix:

Variant related genes	Relation type
C3orf58	TF binding region
C3orf58	CpG island
ENSG00000062716	Chromatin interaction
ENSG00000196233	Chromatin interaction
ENSG00000157593	Chromatin interaction
ENSG00000110700	Chromatin interaction
ENSG00000105771	Chromatin interaction
ENSG00000133639	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000100084	Chromatin interaction
ENSG00000109046	Chromatin interaction
ENSG00000185608	Chromatin interaction
ENSG00000245904	Chromatin interaction
ENSG00000023697	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1027726	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1027727	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1125704	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1125705	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710441	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11720540	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11914522	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13062780	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13083596	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13092757	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13323371	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1354495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1370027	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1370028	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1370029	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370030	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1394399	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1394400	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1394401	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1436629	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1469871	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1504596	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1504600	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs1504601	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1550141	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1550142	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1583550	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1595208	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1595209	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1595210	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1595211	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17603166	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17667256	0.81[CEU][hapmap]
rs1898263	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1992094	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2118071	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2118072	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134914	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134915	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134916	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2164551	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2164552	0.82[EUR][1000 genomes]
rs2164553	0.82[EUR][1000 genomes]
rs2202378	0.84[EUR][1000 genomes]
rs2217926	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2221411	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2361211	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2370174	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2370175	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34200306	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34743418	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35291263	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4258964	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4258965	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4276180	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4334641	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4350918	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4431106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437138	0.86[AMR][1000 genomes]
rs4462961	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4476500	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4549268	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4563410	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4575896	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4582058	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59870355	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440206	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440207	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440208	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440209	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67417607	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6766439	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767811	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6770317	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6798775	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6803148	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs723490	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs723492	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7432451	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7611555	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611648	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611814	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7619036	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7619220	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7622357	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7626898	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628282	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630146	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7638577	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7643341	0.82[ASN][1000 genomes]
rs7643800	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7650233	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7650239	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7650332	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7650459	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651567	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7652490	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7653287	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653431	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289671	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9683376	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9811736	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811888	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9812340	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9812374	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9829883	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9835170	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9840157	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9840519	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9840971	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9841182	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9854844	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9860872	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9865128	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9867025	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9867615	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9867976	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9869178	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9870551	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9872448	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9872595	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876654	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878070	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3349108	chr3:143676303-143692796	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7631704	C3orf58	cis	cerebellum	SCAN
rs7631704	HPS3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143688800-143696400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:143689000-143693200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:143689000-143694400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:143689000-143695400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:143689000-143696800	Active TSS	Stomach Smooth Muscle	stomach
6	chr3:143689200-143693200	Active TSS	A549	lung
7	chr3:143689200-143693400	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:143689200-143693800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:143689200-143694400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:143689200-143695400	Active TSS	K562	blood
11	chr3:143689200-143695800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:143689200-143696200	Active TSS	GM12878-XiMat	blood
13	chr3:143689400-143690600	Active TSS	Brain Germinal Matrix	brain
14	chr3:143689400-143691000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:143689400-143691200	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr3:143689400-143691400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:143689400-143692000	Active TSS	Placenta	Placenta
18	chr3:143689400-143692400	Active TSS	Primary T cells from cord blood	blood
19	chr3:143689400-143692400	Active TSS	Duodenum Mucosa	Duodenum
20	chr3:143689400-143692600	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr3:143689400-143693000	Active TSS	Fetal Kidney	kidney
22	chr3:143689400-143693200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr3:143689400-143693200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:143689400-143693200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:143689400-143693200	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr3:143689400-143693200	Active TSS	Stomach Mucosa	stomach
27	chr3:143689400-143693400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:143689400-143693400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:143689400-143693400	Active TSS	Colon Smooth Muscle	Colon
30	chr3:143689400-143693400	Active TSS	Psoas Muscle	Psoas
31	chr3:143689400-143693400	Active TSS	Right Ventricle	heart
32	chr3:143689400-143693600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:143689400-143693600	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr3:143689400-143693600	Active TSS	Fetal Muscle Trunk	muscle
35	chr3:143689400-143693600	Active TSS	Rectal Smooth Muscle	rectum
36	chr3:143689400-143693600	Active TSS	Thymus	Thymus
37	chr3:143689400-143693600	Active TSS	NHDF-Ad	bronchial
38	chr3:143689400-143693800	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr3:143689400-143693800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:143689400-143694000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:143689400-143694000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:143689400-143694000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr3:143689400-143694000	Active TSS	Fetal Thymus	thymus
44	chr3:143689400-143694200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:143689400-143694200	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr3:143689400-143694200	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr3:143689400-143694400	Active TSS	H1 Cell Line	embryonic stem cell
48	chr3:143689400-143694400	Active TSS	Fetal Muscle Leg	muscle
49	chr3:143689400-143694800	Active TSS	Brain Anterior Caudate	brain
50	chr3:143689400-143695000	Active TSS	Brain Hippocampus Middle	brain

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Variant report

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