Variant report

Variant	rs6438502
Chromosome Location	chr3:118908522-118908523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:118903436..118905729-chr3:118907568..118909269,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114638	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10511382	0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs11927939	0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12634868	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13081519	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829477	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs16829479	1.00[CHB][hapmap]
rs3796356	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796357	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4370022	0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs4687840	0.91[EUR][1000 genomes]
rs4687980	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs4687981	1.00[EUR][1000 genomes]
rs4687982	0.91[EUR][1000 genomes]
rs57258193	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58939003	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61162364	0.82[EUR][1000 genomes]
rs6438506	1.00[CHB][hapmap]
rs7426444	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840317	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv591361	chr3:118901832-118909987	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv527259	chr3:118906442-118916627	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv591362	chr3:118906442-118948155	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118884000-118914200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:118901000-118924200	Weak transcription	Pancreas	Pancrea
3	chr3:118903400-118924200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:118903800-118908600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:118904400-118910600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:118904400-118912800	Weak transcription	NH-A	brain
7	chr3:118904400-118913000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:118904600-118936400	Weak transcription	Gastric	stomach
9	chr3:118904800-118910400	Weak transcription	HMEC	breast
10	chr3:118904800-118913000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:118904800-118914400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:118906800-118909400	Enhancers	A549	lung
13	chr3:118906800-118910400	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr3:118907000-118910600	Weak transcription	Placenta	Placenta
15	chr3:118907600-118910600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:118908000-118908600	ZNF genes & repeats	Aorta	Aorta
17	chr3:118908000-118908600	Enhancers	Left Ventricle	heart
18	chr3:118908200-118908600	Enhancers	Right Ventricle	heart
19	chr3:118908200-118908800	Enhancers	Fetal Heart	heart
20	chr3:118908200-118909000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:118908400-118910800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:118908400-118928200	Weak transcription	Fetal Stomach	stomach

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