Variant report

Variant	rs3757393
Chromosome Location	chr7:137759000-137759001
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	SETDB1	chr7:137758718-137759262	U2OS	brain:	n/a	n/a
2	FOXA2	chr7:137758730-137759115	A549	lung:	n/a	n/a
3	FOS	chr7:137758933-137759202	MCF10A-Er-Src	breast:	n/a	n/a
4	FOXA1	chr7:137758772-137759139	HepG2	liver:	n/a	chr7:137759052-137759067
5	FOXA1	chr7:137758780-137759102	T-47D	breast:	n/a	chr7:137759052-137759067
6	EP300	chr7:137758684-137759134	HepG2	liver:	n/a	n/a
7	KAP1	chr7:137758709-137759126	HEK293	kidney:	n/a	n/a
8	NR2F2	chr7:137758682-137759588	MCF-7	breast:	n/a	n/a
9	FOXA1	chr7:137758666-137759208	HepG2	liver:	n/a	chr7:137759052-137759067
10	GATA3	chr7:137758629-137759614	MCF-7	breast:	n/a	n/a
11	FOXA1	chr7:137758726-137759057	T-47D	breast:	n/a	n/a
12	EP300	chr7:137758756-137759415	MCF-7	breast:	n/a	n/a
13	CEBPB	chr7:137758776-137759144	MCF-7	breast:	n/a	n/a
14	FOXA2	chr7:137758680-137759253	A549	lung:	n/a	n/a
15	FOXA2	chr7:137758705-137759138	HepG2	liver:	n/a	n/a
16	FOXA1	chr7:137758708-137759190	HepG2	liver:	n/a	chr7:137759052-137759067

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:137747667..137753748-chr7:137756655..137760355,9	MCF-7	breast:

Variant related genes	Relation type
AKR1D1	TF binding region
ENSG00000221558	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10246884	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1025967	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10264658	0.92[EUR][1000 genomes]
rs10280394	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10280628	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10954602	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11982192	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs13243992	0.92[EUR][1000 genomes]
rs1424379	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1424380	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1872929	0.90[GIH][hapmap]
rs1872930	0.90[GIH][hapmap]
rs2120846	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2166188	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306847	0.87[GIH][hapmap]
rs2859828	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807332	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4732285	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6945659	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6977075	0.86[CEU][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs6980334	0.86[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs7784881	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7787591	0.92[EUR][1000 genomes]
rs7795946	0.86[CEU][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518070	chr7:137534627-137808839	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv831151	chr7:137711447-137865471	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	nsv437032	chr7:137753091-137773291	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137757600-137759600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
2	chr7:137757800-137761200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
3	chr7:137758000-137760200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr7:137758600-137759800	Enhancers	HMEC	breast
5	chr7:137758600-137761200	ZNF genes & repeats	HepG2	liver
6	chr7:137758800-137759200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:137758800-137759200	Flanking Active TSS	Liver	Liver
8	chr7:137758800-137759400	Enhancers	Hela-S3	cervix
9	chr7:137759000-137760600	Enhancers	Primary B cells from peripheral blood	blood

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