Variant report

Variant	rs6779394
Chromosome Location	chr3:49157771-49157772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:62)
CpG islands
(count:61)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:62 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr3:49157619-49158720	SK-N-SH	brain:	n/a	chr3:49158511-49158520
2	POLR2A	chr3:49157377-49158390	IMR90	lung:	n/a	n/a
3	POLR2A	chr3:49157437-49157814	U87	brain:	n/a	n/a
4	HCFC1	chr3:49157317-49159219	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:49157467-49158982	HL-60	blood:	n/a	n/a
6	POLR2A	chr3:49157545-49158554	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:49157439-49158767	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr3:49157660-49157810	GM12864	blood:	n/a	n/a
9	ELF1	chr3:49157670-49159107	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:49157685-49158696	A549	lung:	n/a	n/a
11	CHD1	chr3:49157668-49158251	GM12878	blood:	n/a	n/a
12	RUNX3	chr3:49157670-49158500	GM12878	blood:	n/a	n/a
13	CTCF	chr3:49157640-49157790	GM12873	blood:	n/a	n/a
14	GABPA	chr3:49157689-49158684	HL-60	blood:	n/a	chr3:49158511-49158520
15	POLR2A	chr3:49156663-49159063	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr3:49157060-49158670	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:49157545-49159020	Raji	blood:	n/a	n/a
18	CTCF	chr3:49157700-49157850	GM12872	blood:	n/a	n/a
19	HEY1	chr3:49157345-49158425	K562	blood:	n/a	chr3:49158120-49158135 chr3:49158119-49158134
20	POLR2A	chr3:49157599-49158551	Hela-S3	cervix:	n/a	n/a
21	TAF1	chr3:49157589-49158579	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr3:49157098-49158591	GM12892	blood:	n/a	n/a
23	GABPA	chr3:49157715-49158650	MCF-7	breast:	n/a	chr3:49158511-49158520
24	POLR2A	chr3:49157476-49157806	K562	blood:	n/a	n/a
25	ESRRA	chr3:49157227-49158852	GM12878	blood:	n/a	chr3:49158105-49158117 chr3:49158105-49158115 chr3:49158104-49158117 chr3:49158105-49158115
26	MAZ	chr3:49157530-49159030	IMR90	lung:	n/a	chr3:49158510-49158520
27	POLR2A	chr3:49157699-49158750	Hela-S3	cervix:	n/a	n/a
28	REST	chr3:49157424-49158816	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr3:49157343-49158640	HUVEC	blood vessel:	n/a	n/a
30	ZNF263	chr3:49156913-49158359	HEK293-T-REx	kidney:	n/a	chr3:49157690-49157699
31	CTCF	chr3:49157680-49157830	HBMEC	blood vessel:	n/a	n/a
32	POLR2A	chr3:49157618-49158577	GM12891	blood:	n/a	n/a
33	CTCF	chr3:49157680-49157830	GM12864	blood:	n/a	n/a
34	POLR2A	chr3:49157619-49158770	GM12878	blood:	n/a	n/a
35	CHD1	chr3:49157350-49158591	IMR90	lung:	n/a	n/a
36	MAX	chr3:49157580-49158947	HepG2	liver:	n/a	chr3:49158510-49158520
37	POLR2A	chr3:49156832-49158778	K562	blood:	n/a	n/a
38	POLR2A	chr3:49157425-49158594	GM12892	blood:	n/a	n/a
39	RFX5	chr3:49157454-49158709	Hela-S3	cervix:	n/a	chr3:49158219-49158234
40	GABPA	chr3:49157588-49158721	A549	lung:	n/a	chr3:49158511-49158520
41	RUNX3	chr3:49157554-49158553	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:49157542-49158600	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr3:49157723-49158773	MCF-7	breast:	n/a	n/a
44	CREB1	chr3:49157753-49158851	HepG2	liver:	n/a	n/a
45	CTCF	chr3:49157740-49157890	GM12870	blood:	n/a	n/a
46	MTA3	chr3:49157183-49158837	GM12878	blood:	n/a	n/a
47	GABPA	chr3:49157667-49158710	SK-N-SH	brain:	n/a	chr3:49158511-49158520
48	POLR2A	chr3:49157725-49158721	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr3:49157580-49158633	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr3:49156840-49158733	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49157769-49157819	PrEC	prostate:	n/a
2	chr3:49157769-49157819	SK-N-SH_RA	brain:	n/a
3	chr3:49157769-49157819	HEK293	kidney:	embryo
4	chr3:49157769-49157819	HRCEpiC	kidney:	n/a
5	chr3:49157769-49157819	GM12878	blood:	n/a
6	chr3:49157769-49157819	Hela-S3	cervix:	n/a
7	chr3:49157769-49157819	K562	blood:	n/a
8	chr3:49157769-49157819	Hepatocyte	liver:	n/a
9	chr3:49157769-49157819	HRE	kidney:	n/a
10	chr3:49157769-49157819	RPTEC	kidney:	n/a
11	chr3:49157769-49157819	NHBE	bronchial:	n/a
12	chr3:49157769-49157819	MCF10A-Er-Src	breast:	n/a
13	chr3:49157769-49157819	AG09319	gingival:	n/a
14	chr3:49157769-49157819	PANC-1	pancreas:	n/a
15	chr3:49157769-49157819	PFSK-1	brain:	n/a
16	chr3:49157769-49157819	SKMC	muscle:	n/a
17	chr3:49157769-49157819	A549	lung:	n/a
18	chr3:49157769-49157819	NH-A	brain:	n/a
19	chr3:49157769-49157819	BE2_C	brain:	n/a
20	chr3:49157769-49157819	NHDF-neo	bronchial:	n/a
21	chr3:49157769-49157819	Caco-2	colon:	n/a
22	chr3:49157769-49157819	HRPEpiC	eye:	n/a
23	chr3:49157769-49157819	HCF	heart:	n/a
24	chr3:49157769-49157819	SK-N-SH	brain:	n/a
25	chr3:49157769-49157819	HIPEpiC	eye:	n/a
26	chr3:49157769-49157819	HUVEC	blood vessel:	n/a
27	chr3:49157769-49157819	HEEpiC	esophagus:	n/a
28	chr3:49157769-49157819	HPAEpiC	pulmonary alveolar:	n/a
29	chr3:49157769-49157819	T-47D	breast:	n/a
30	chr3:49157769-49157819	AG04449	skin:	fetal
31	chr3:49157769-49157819	AG09309	skin:	n/a
32	chr3:49157769-49157819	LNCaP	prostate:	n/a
33	chr3:49157769-49157819	NB4	blood:	n/a
34	chr3:49157769-49157819	GM12892	blood:	n/a
35	chr3:49157769-49157819	SK-N-MC	brain:	n/a
36	chr3:49157769-49157819	CMK	blood:	n/a
37	chr3:49157769-49157819	AG10803	skin:	n/a
38	chr3:49157769-49157819	HNPCEpiC	eye:	n/a
39	chr3:49157769-49157819	MCF-7	breast:	n/a
40	chr3:49157769-49157819	GM19239	blood:	n/a
41	chr3:49157769-49157819	AG04450	lung:	fetal
42	chr3:49157769-49157819	IMR90	lung:	fetal
43	chr3:49157769-49157819	GM12891	blood:	n/a
44	chr3:49157769-49157819	HMEC	breast:	n/a
45	chr3:49157769-49157819	AoSMC	blood vessel:	n/a
46	chr3:49157769-49157819	HL-60	blood:	n/a
47	chr3:49157769-49157819	H1-hESC	embryonic stem cell:	embryo
48	chr3:49157769-49157819	HAEpiC	amniotic membrane:	n/a
49	chr3:49157769-49157819	ECC-1	luminal epithelium:	n/a
50	chr3:49157769-49157819	HCM	heart:	n/a

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49065059..49067026-chr3:49155919..49158301,2	MCF-7	breast:
2	chr3:49057883..49060618-chr3:49157462..49160241,4	MCF-7	breast:
3	chr3:49056273..49062188-chr3:49155312..49159947,7	K562	blood:
4	chr3:49064025..49068089-chr3:49156559..49161197,7	MCF-7	breast:
5	chr3:49128926..49138937-chr3:49145476..49160975,31	K562	blood:
6	chr3:49141581..49143765-chr3:49156175..49158476,2	K562	blood:
7	chr3:49134791..49138406-chr3:49156749..49159761,5	K562	blood:
8	chr3:49157336..49159924-chr3:49160004..49161894,2	MCF-7	breast:
9	chr3:49156732..49159393-chr3:49207552..49211410,3	K562	blood:
10	chr3:49058620..49061371-chr3:49155094..49159079,3	MCF-7	breast:
11	chr3:49057812..49061431-chr3:49156444..49158785,4	K562	blood:
12	chr3:49129847..49133782-chr3:49155056..49162049,12	MCF-7	breast:
13	chr3:49156700..49159998-chr3:49200731..49203876,4	MCF-7	breast:
14	chr3:49151622..49155805-chr3:49155952..49160094,9	K562	blood:
15	chr3:49056021..49057795-chr3:49157491..49159420,2	MCF-7	breast:
16	chr3:49157716..49158699-chr5:98264536..98265045,2	HCT-116	colon:
17	chr3:49128925..49131724-chr3:49157587..49160255,2	MCF-7	breast:
18	chr3:49140522..49142254-chr3:49155638..49159426,3	MCF-7	breast:
19	chr3:49155392..49161176-chr3:49167558..49172640,8	MCF-7	breast:
20	chr3:49144707..49154191-chr3:49155059..49160099,12	MCF-7	breast:
21	chr3:49051266..49053543-chr3:49156986..49159696,2	MCF-7	breast:
22	chr3:49155018..49163811-chr3:49167026..49172599,15	MCF-7	breast:
23	chr3:49148095..49150298-chr3:49155546..49158481,2	K562	blood:

No data

Variant related genes	Relation type
USP19	TF binding region
USP19	CpG island
ENSG00000207605	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000248489	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000178252	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 38 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10049462	1.00[JPT][hapmap]
rs10154895	0.89[ASN][1000 genomes]
rs10865954	1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[ASN][1000 genomes]
rs11130184	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs1134591	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap]
rs11552724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11706052	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11706189	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11712006	1.00[ASN][1000 genomes]
rs11713297	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11715581	0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11716334	0.82[ASN][1000 genomes]
rs11719220	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11920267	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12487580	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12490393	0.82[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12491743	0.83[AMR][1000 genomes]
rs12493001	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12629759	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs12631989	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs12636030	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12637037	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12637576	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs13064784	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13068038	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs13072554	0.87[ASN][1000 genomes]
rs13077498	1.00[JPT][hapmap]
rs13080725	0.87[ASN][1000 genomes]
rs13086240	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13087930	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs13092715	0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs13096406	0.81[ASN][1000 genomes]
rs13315711	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs13316620	0.92[CEU][hapmap];0.81[AFR][1000 genomes]
rs2117938	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs2304442	1.00[JPT][hapmap]
rs3212	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34326553	1.00[ASN][1000 genomes]
rs34566463	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs34580506	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34889065	1.00[ASN][1000 genomes]
rs35060561	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35102816	0.84[ASN][1000 genomes]
rs35108630	0.87[ASN][1000 genomes]
rs35174559	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs35283189	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35673421	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs36133651	0.92[EUR][1000 genomes]
rs3774800	0.92[CEU][hapmap]
rs3923475	0.87[ASN][1000 genomes]
rs4072859	0.81[AFR][1000 genomes]
rs4279134	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4292260	0.81[ASW][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs4308307	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4364202	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4499638	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4513485	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4521268	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4536858	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4955410	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4955411	0.81[ASW][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs4955416	0.81[ASW][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs4955418	0.82[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4955419	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4955420	1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs4955432	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs4974080	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs4974082	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs5030795	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55713230	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61583136	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62262517	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6414613	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs6446196	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs6446205	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs66991555	0.84[ASN][1000 genomes]
rs6768433	0.95[CEU][hapmap]
rs6770112	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6772452	0.82[LWK][hapmap];0.86[YRI][hapmap]
rs6781790	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap]
rs6784111	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6789285	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6790914	0.87[ASN][1000 genomes]
rs6794924	0.82[ASN][1000 genomes]
rs6795025	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7373072	0.88[YRI][hapmap]
rs7373790	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7430198	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs7432989	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7615235	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7617480	0.93[YRI][hapmap]
rs7621015	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap]
rs7626445	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628719	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs7632267	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7643368	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap]
rs7645551	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7652746	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs9311439	1.00[JPT][hapmap]
rs9586	0.89[YRI][hapmap]
rs9637481	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9683094	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9814987	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9831648	0.93[YRI][hapmap]
rs9835439	0.89[ASN][1000 genomes]
rs9837237	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9837625	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9840050	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9846123	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9847839	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9850917	1.00[JPT][hapmap]
rs9855123	0.89[ASN][1000 genomes]
rs9862483	0.89[ASN][1000 genomes]
rs9880088	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9880309	1.00[JPT][hapmap]
rs9990153	0.87[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:38)

SNP	Gene	Cis/trans	Tissue	Source
rs6779394	NICN1	cis	Thyroid	GTEx
rs6779394	PHF7	cis	parietal	SCAN
rs6779394	NICN1-AS1	cis	Thyroid	GTEx
rs6779394	DALRD3	cis	cerebellum	SCAN
rs6779394	AMT	cis	Whole Blood	GTEx
rs6779394	DALRD3	cis	parietal	SCAN
rs6779394	CCDC71	cis	cerebellum	SCAN
rs6779394	WDR6	cis	Muscle Skeletal	GTEx
rs6779394	WDR6	cis	Heart Left Ventricle	GTEx
rs6779394	AMT	cis	Muscle Skeletal	GTEx
rs6779394	NCKIPSD	cis	parietal	SCAN
rs6779394	P4HTM	cis	parietal	SCAN
rs6779394	NCKIPSD	cis	Whole Blood	GTEx
rs6779394	WDR6	cis	lymphoblastoid	seeQTL
rs6779394	AMT	cis	cerebellum	SCAN
rs6779394	CCDC36	cis	Artery Tibial	GTEx
rs6779394	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs6779394	WDR6	cis	Nerve Tibial	GTEx
rs6779394	WDR6	cis	Artery Tibial	GTEx
rs6779394	CCDC36	cis	Esophagus Muscularis	GTEx
rs6779394	NCKIPSD	cis	Muscle Skeletal	GTEx
rs6779394	WDR6	cis	cerebellum	SCAN
rs6779394	WDR6	cis	Whole Blood	GTEx
rs6779394	WDR6	cis	Esophagus Muscularis	GTEx
rs6779394	NCKIPSD	cis	cerebellum	SCAN
rs6779394	TLR9	cis	parietal	SCAN
rs6779394	NCKIPSD	cis	Nerve Tibial	GTEx
rs6779394	AMT	cis	Thyroid	GTEx
rs6779394	WDR6	cis	Adipose Subcutaneous	GTEx
rs6779394	P4HTM	cis	cerebellum	SCAN
rs6779394	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6779394	WDR6	cis	uninvolved skin	skin_eQTL
rs6779394	WDR6	cis	Stomach	GTEx
rs6779394	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs6779394	WDR6	cis	lung	GTEx
rs6779394	AMT	cis	parietal	SCAN
rs6779394	WDR6	cis	parietal	SCAN
rs6779394	WDR6	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49156000-49162600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:49156400-49158200	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr3:49156600-49157800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr3:49156600-49157800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:49156600-49157800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr3:49156600-49157800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr3:49156600-49158000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:49156600-49158800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
9	chr3:49156800-49157800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49156800-49157800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:49156800-49157800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr3:49156800-49157800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr3:49156800-49157800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr3:49156800-49157800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:49156800-49157800	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr3:49156800-49157800	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr3:49156800-49157800	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr3:49156800-49157800	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr3:49156800-49157800	Flanking Active TSS	Fetal Lung	lung
20	chr3:49156800-49157800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:49156800-49157800	Flanking Active TSS	NHEK	skin
22	chr3:49156800-49157800	Flanking Active TSS	NHLF	lung
23	chr3:49156800-49157800	Flanking Active TSS	Osteobl	bone
24	chr3:49156800-49158000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:49156800-49158000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:49156800-49158000	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr3:49156800-49158000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
28	chr3:49156800-49158000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr3:49156800-49158000	Flanking Active TSS	Fetal Brain Female	brain
30	chr3:49156800-49158000	Flanking Active TSS	NH-A	brain
31	chr3:49156800-49158200	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr3:49156800-49158200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:49156800-49158800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:49157000-49157800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:49157000-49157800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr3:49157000-49157800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr3:49157000-49157800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr3:49157000-49157800	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr3:49157000-49157800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:49157000-49157800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
41	chr3:49157000-49157800	Flanking Active TSS	Pancreas	Pancrea
42	chr3:49157000-49157800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr3:49157000-49157800	Flanking Active TSS	Stomach Mucosa	stomach
44	chr3:49157000-49158000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr3:49157000-49158000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr3:49157000-49158000	Flanking Active TSS	HMEC	breast
47	chr3:49157000-49158200	Flanking Active TSS	Colonic Mucosa	Colon
48	chr3:49157000-49158800	Active TSS	H9 Cell Line	embryonic stem cell
49	chr3:49157200-49157800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:49157200-49157800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links