Variant report

Variant	rs12529631
Chromosome Location	chr6:88136554-88136555
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	GATA3	chr6:88136520-88136967	MCF-7	breast:	n/a	chr6:88136802-88136818 chr6:88136806-88136813 chr6:88136806-88136815
2	CEBPB	chr6:88136515-88136956	MCF-7	breast:	n/a	n/a
3	ATF1	chr6:88136539-88136798	K562	blood:	n/a	n/a
4	SIN3AK20	chr6:88136526-88136957	MCF-7	breast:	n/a	n/a
5	GATA3	chr6:88136512-88136968	MCF-7	breast:	n/a	chr6:88136802-88136818 chr6:88136806-88136813 chr6:88136806-88136815
6	NR2F2	chr6:88136448-88136852	MCF-7	breast:	n/a	chr6:88136700-88136715

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88136188..88139146-chr6:88139445..88141590,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000216324	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12178951	1.00[EUR][1000 genomes]
rs12528249	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12529035	1.00[YRI][hapmap]
rs12529618	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12530034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192579	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13195057	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13196020	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13197065	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13198605	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13205397	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13217556	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13217637	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13218502	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13219364	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13220737	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16879293	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16879295	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2875534	0.85[EUR][1000 genomes]
rs34144911	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34294674	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34373986	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34592526	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34726630	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34914404	0.85[EUR][1000 genomes]
rs35243146	1.00[AMR][1000 genomes]
rs35562204	0.82[EUR][1000 genomes]
rs35580717	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35756344	0.85[EUR][1000 genomes]
rs35822597	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45563737	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58735049	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60711734	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6454604	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs66632635	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66786089	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66805147	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66819255	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67569613	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67776922	0.85[EUR][1000 genomes]
rs68100217	1.00[EUR][1000 genomes]
rs6939602	1.00[CHD][hapmap]
rs71572754	0.83[AMR][1000 genomes]
rs71572755	0.85[EUR][1000 genomes]
rs71572757	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71572758	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71572762	0.85[EUR][1000 genomes]

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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88135800-88137400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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