Variant report

Variant	rs12652479
Chromosome Location	chr5:57050359-57050360
allele	A/C
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	STAT3	chr5:57050318-57050874	MCF10A-Er-Src	breast:	n/a	chr5:57050552-57050561 chr5:57050572-57050580 chr5:57050419-57050442 chr5:57050419-57050427
2	STAT3	chr5:57050294-57050910	MCF10A-Er-Src	breast:	n/a	chr5:57050890-57050897 chr5:57050552-57050561 chr5:57050572-57050580 chr5:57050419-57050442 chr5:57050419-57050427

Variant related genes	Relation type
ENSG00000249198	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10063478	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10077188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12153068	0.83[EUR][1000 genomes]
rs12189365	0.83[EUR][1000 genomes]
rs12654351	0.83[EUR][1000 genomes]
rs12654850	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12654963	0.83[EUR][1000 genomes]
rs12655658	0.83[EUR][1000 genomes]
rs12657522	0.84[YRI][hapmap]
rs12658410	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658940	0.83[EUR][1000 genomes]
rs4700209	0.83[EUR][1000 genomes]
rs59516621	0.83[EUR][1000 genomes]
rs60219417	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61220614	0.83[EUR][1000 genomes]
rs6876911	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73085594	0.83[EUR][1000 genomes]
rs73089817	0.83[EUR][1000 genomes]
rs73089845	0.83[EUR][1000 genomes]
rs73089868	0.83[EUR][1000 genomes]
rs73089871	0.88[AFR][1000 genomes]
rs73089872	0.83[EUR][1000 genomes]
rs73089877	0.83[EUR][1000 genomes]
rs73089897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089900	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7702309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7729312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7731160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7734787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57045400-57054800	Weak transcription	Pancreas	Pancrea
2	chr5:57046000-57050800	Weak transcription	Osteobl	bone
3	chr5:57047200-57051200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:57048600-57050400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:57048600-57050600	Enhancers	HMEC	breast
6	chr5:57048600-57051000	Enhancers	NHEK	skin
7	chr5:57049000-57050800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:57049600-57051000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:57050200-57050400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:57050200-57051200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr5:57050200-57051400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:57050200-57051400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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