Variant report

Variant	rs12639236
Chromosome Location	chr3:161019561-161019562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:161015254..161017853-chr3:161017997..161020969,3	MCF-7	breast:
2	chr3:161008825..161011229-chr3:161019509..161021871,2	MCF-7	breast:
3	chr3:160940415..160942308-chr3:161018142..161020676,2	MCF-7	breast:
4	chr3:161017448..161020301-chr3:161062969..161065681,2	MCF-7	breast:
5	chr3:161016261..161017784-chr3:161018167..161020383,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12631095	0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631808	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632351	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632514	1.00[EUR][1000 genomes]
rs12632632	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632686	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634108	1.00[EUR][1000 genomes]
rs12634781	0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12635895	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12636473	1.00[EUR][1000 genomes]
rs16832385	1.00[EUR][1000 genomes]
rs2404345	1.00[EUR][1000 genomes]
rs34868645	1.00[EUR][1000 genomes]
rs55914832	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56230831	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56378191	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57175632	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57212203	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58013864	1.00[EUR][1000 genomes]
rs58404146	1.00[EUR][1000 genomes]
rs58550445	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60172527	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61631170	1.00[EUR][1000 genomes]
rs72494862	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72494864	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73021435	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73875481	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875497	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875623	1.00[EUR][1000 genomes]
rs73878306	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73878333	1.00[EUR][1000 genomes]
rs73878336	1.00[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv4091	chr3:161018540-161063875	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161017000-161021400	Weak transcription	Aorta	Aorta
2	chr3:161017000-161033000	Weak transcription	Left Ventricle	heart
3	chr3:161017200-161019600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:161017200-161020800	Weak transcription	Pancreas	Pancrea
5	chr3:161017600-161032600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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