Variant report

Variant	rs1038394
Chromosome Location	chr3:47464122-47464123
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	RAD21	chr3:47463878-47464187	H1-hESC	embryonic stem cell:	n/a	chr3:47463906-47463916
2	RAD21	chr3:47463852-47464180	HepG2	liver:	n/a	chr3:47463906-47463916
3	CTCF	chr3:47463860-47464169	MCF-7	breast:	n/a	n/a
4	CTCF	chr3:47463929-47464133	ProgFib	skin:	n/a	n/a
5	POLR2A	chr3:47463929-47464134	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr3:47463890-47464161	NHEK	skin:	n/a	n/a
7	CTCF	chr3:47464000-47464150	Hela-S3	cervix:	n/a	n/a
8	MYC	chr3:47463935-47464322	A549	lung:	n/a	chr3:47464054-47464064
9	RAD21	chr3:47462394-47464375	SK-N-SH	brain:	n/a	chr3:47463906-47463916
10	CTCF	chr3:47463832-47464255	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:47463171-47464147	HepG2	liver:	n/a	n/a
12	MYC	chr3:47463877-47464221	MCF10A-Er-Src	breast:	n/a	chr3:47464054-47464064
13	POLR2A	chr3:47463782-47464311	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr3:47463980-47464130	SK-N-SH_RA	brain:	n/a	n/a
15	SMC3	chr3:47463931-47464138	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr3:47463980-47464130	HMEC	breast:	n/a	n/a
17	CTCF	chr3:47464000-47464150	A549	lung:	n/a	n/a
18	CTCF	chr3:47463913-47464136	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr3:47463980-47464130	GM12878	blood:	n/a	n/a
20	CTCF	chr3:47463921-47464124	Pancreas_OC	pancreas:	n/a	n/a
21	MAX	chr3:47463888-47464205	Hela-S3	cervix:	n/a	chr3:47464054-47464064
22	ZNF263	chr3:47463385-47464275	HEK293-T-REx	kidney:	n/a	n/a
23	CTCF	chr3:47463905-47464170	GM12892	blood:	n/a	n/a
24	CTCF	chr3:47463876-47464197	A549	lung:	n/a	n/a
25	CTCF	chr3:47463980-47464130	A549	lung:	n/a	n/a
26	POLR2A	chr3:47463744-47464185	U87	brain:	n/a	n/a
27	FOS	chr3:47463984-47464172	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr3:47463597-47464208	ECC-1	luminal epithelium:	n/a	n/a
29	MYC	chr3:47463909-47464178	MCF-7	breast:	n/a	chr3:47464054-47464064
30	CTCF	chr3:47464020-47464170	HFF	foreskin:	n/a	n/a
31	MAX	chr3:47463875-47464500	NB4	blood:	n/a	chr3:47464415-47464426 chr3:47464054-47464064
32	CTCF	chr3:47463875-47464165	GM12891	blood:	n/a	n/a
33	CTCF	chr3:47463980-47464130	GM12873	blood:	n/a	n/a
34	POLR2A	chr3:47461850-47464718	A549	lung:	n/a	n/a
35	MYC	chr3:47463925-47464201	Hela-S3	cervix:	n/a	chr3:47464054-47464064
36	CTCF	chr3:47464020-47464170	HMEC	breast:	n/a	n/a
37	CTCF	chr3:47463980-47464130	AG09309	skin:	n/a	n/a
38	RAD21	chr3:47463772-47464242	H1-hESC	embryonic stem cell:	n/a	chr3:47463906-47463916
39	CTCF	chr3:47463651-47464372	A549	lung:	n/a	n/a
40	MYC	chr3:47464029-47464161	HUVEC	blood vessel:	n/a	chr3:47464054-47464064
41	CTCF	chr3:47463891-47464215	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr3:47463887-47464169	MCF-7	breast:	n/a	n/a
43	MAX	chr3:47463917-47464193	K562	blood:	n/a	chr3:47464054-47464064
44	MYC	chr3:47463849-47464229	MCF-7	breast:	n/a	chr3:47464054-47464064
45	CTCF	chr3:47463980-47464130	HAc	cerebellar:	n/a	n/a
46	CTCF	chr3:47463980-47464130	HVMF	connective:	n/a	n/a
47	CTCF	chr3:47463980-47464130	HFF-Myc	foreskin:	n/a	n/a
48	CTCF	chr3:47463876-47464141	Fibrobl	skin:	n/a	n/a
49	FOSL2	chr3:47463882-47464260	A549	lung:	n/a	n/a
50	CTCF	chr3:47463980-47464130	AG10803	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47421777..47424260-chr3:47463551..47466510,3	MCF-7	breast:
2	chr3:47461509..47464905-chr3:47467197..47468812,4	K562	blood:
3	chr3:47462501..47465704-chr3:47552223..47556756,6	MCF-7	breast:
4	chr3:47463918..47464503-chr3:47554835..47555904,4	MCF-7	breast:
5	chr3:47462410..47464482-chr3:47553675..47556809,5	MCF-7	breast:
6	chr3:47463570..47464475-chr3:47516993..47518028,5	MCF-7	breast:
7	chr3:47463544..47464124-chr3:47517490..47518060,2	MCF-7	breast:

Variant related genes	Relation type
SCAP	TF binding region
ENSG00000114650	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000260236	Chromatin interaction
ENSG00000163832	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1076394	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs10865946	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130123	0.92[CEU][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap]
rs11130124	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11130126	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs11130127	0.86[EUR][1000 genomes]
rs11130128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130129	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130132	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130133	0.82[EUR][1000 genomes]
rs11130137	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs11705957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11710013	0.96[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap]
rs11710121	0.88[CEU][hapmap]
rs11710322	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11711265	0.86[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs11711824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712445	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11716763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11719877	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11914913	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11914932	0.82[EUR][1000 genomes]
rs11915074	0.88[CEU][hapmap]
rs11920853	0.88[CEU][hapmap]
rs11925823	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11927371	0.82[EUR][1000 genomes]
rs12486969	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12487736	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12489046	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12490058	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12492433	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12495169	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs12497225	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12630641	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12632132	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12636851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13064843	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13075233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13079098	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13094438	0.96[CEU][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap]
rs1531875	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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1564760	0.90[YRI][hapmap]
rs1638676	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs17080872	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs17410853	0.88[CEU][hapmap]
rs17411375	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs17784882	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs1872164	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2062278	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2101247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2159400	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2276853	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2276854	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2291298	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs295428	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs295433	0.95[YRI][hapmap]
rs295441	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap]
rs295442	0.96[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs295449	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs295458	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs295461	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3736177	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816779	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4241548	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683326	0.96[CEU][hapmap]
rs4858805	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858848	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858856	0.80[EUR][1000 genomes]
rs4858868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858888	0.86[EUR][1000 genomes]
rs4858890	0.81[EUR][1000 genomes]
rs4858893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4858894	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs553989	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56032309	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56351005	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57346147	0.97[EUR][1000 genomes]
rs59586735	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60369822	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62246474	0.86[EUR][1000 genomes]
rs62248580	0.88[EUR][1000 genomes]
rs62248599	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62248603	0.82[EUR][1000 genomes]
rs62248605	0.82[EUR][1000 genomes]
rs62260710	0.81[EUR][1000 genomes]
rs62260711	0.81[EUR][1000 genomes]
rs6765990	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6768221	0.88[CEU][hapmap]
rs6780013	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs6787422	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6791842	0.96[CEU][hapmap]
rs6792461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6792488	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6800271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73081205	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7613282	0.85[EUR][1000 genomes]
rs7628631	0.82[EUR][1000 genomes]
rs7641010	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7649234	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651194	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807810	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs807931	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs807932	0.92[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap]
rs807936	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs811115	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap]
rs8180040	0.84[EUR][1000 genomes]
rs878659	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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs922957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9683033	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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9683177	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1038394	AMIGO3	cis	cerebellum	SCAN
rs1038394	IFRD2	cis	parietal	SCAN
rs1038394	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs1038394	QRICH1	cis	parietal	SCAN
rs1038394	CCDC12	cis	cerebellum	SCAN
rs1038394	PRKAR2A	cis	cerebellum	SCAN
rs1038394	C3orf75	cis	cerebellum	SCAN
rs1038394	SCAP	cis	parietal	SCAN
rs1038394	HYAL2	cis	cerebellum	SCAN
rs1038394	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47441000-47476800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:47448400-47466000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:47450400-47484800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:47451400-47466400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:47454600-47466800	Weak transcription	Psoas Muscle	Psoas
6	chr3:47456000-47473000	Strong transcription	Thymus	Thymus
7	chr3:47459200-47465200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:47459600-47470000	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr3:47460400-47470400	Strong transcription	NHEK	skin
10	chr3:47461000-47466600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:47461200-47465400	Genic enhancers	Right Ventricle	heart
12	chr3:47461800-47467000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:47461800-47478800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:47462000-47464800	Genic enhancers	Spleen	Spleen
15	chr3:47462200-47464800	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr3:47462400-47464400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:47462400-47464600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:47462400-47464600	Enhancers	Fetal Heart	heart
19	chr3:47462400-47464600	Genic enhancers	Pancreas	Pancrea
20	chr3:47462400-47464600	Genic enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:47462400-47464800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:47462400-47464800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:47462400-47465400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:47462400-47467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:47462600-47464200	Genic enhancers	Brain Cingulate Gyrus	brain
26	chr3:47462600-47464600	Enhancers	Left Ventricle	heart
27	chr3:47462600-47465600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:47462600-47465800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:47462600-47466800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:47462800-47464400	Genic enhancers	Esophagus	oesophagus
31	chr3:47462800-47464600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:47462800-47465800	Genic enhancers	HepG2	liver
33	chr3:47462800-47466800	Enhancers	Stomach Mucosa	stomach
34	chr3:47463000-47464200	Enhancers	Lung	lung
35	chr3:47463000-47464200	Enhancers	Ovary	ovary
36	chr3:47463000-47464600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:47463000-47469800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:47463000-47470200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:47463000-47470600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:47463000-47485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:47463200-47464400	Genic enhancers	Rectal Mucosa Donor 29	rectum
42	chr3:47463200-47464400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:47463200-47464600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:47463200-47464600	Weak transcription	Primary B cells from cord blood	blood
45	chr3:47463200-47464600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:47463200-47464600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:47463200-47464600	Genic enhancers	Colonic Mucosa	Colon
48	chr3:47463200-47464600	Genic enhancers	Gastric	stomach
49	chr3:47463200-47465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:47463200-47465200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links