Variant report

Variant	rs1867829
Chromosome Location	chr2:113839151-113839152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113838578..113840540-chr2:113849414..113851474,2	MCF-7	breast:
2	chr2:113836939..113839548-chr2:113991525..113994507,2	MCF-7	breast:
3	chr2:113835964..113840226-chr2:113955452..113959687,5	MCF-7	breast:
4	chr2:113837765..113839725-chr2:113955649..113957205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125618	Chromatin interaction
ENSG00000189223	Chromatin interaction
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11123162	0.90[JPT][hapmap]
rs12475887	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13032281	0.92[ASN][1000 genomes]
rs1618084	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1630153	0.81[JPT][hapmap]
rs1665189	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1688075	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1688076	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1794071	0.94[ASN][1000 genomes]
rs28928309	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs315925	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs315927	0.81[JPT][hapmap]
rs315929	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs315931	0.81[JPT][hapmap]
rs315932	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4848314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849148	0.88[GIH][hapmap]
rs4849152	0.81[JPT][hapmap]
rs4849153	0.90[JPT][hapmap]
rs4989179	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55932259	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56011414	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57130564	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158848	0.95[ASN][1000 genomes]
rs66613854	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66615594	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9308682	0.88[GIH][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv2881	chr2:113800805-113846597	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113825800-113839600	Enhancers	HMEC	breast
2	chr2:113834600-113840000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:113838000-113839400	Enhancers	Esophagus	oesophagus
4	chr2:113838200-113842200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:113838200-113842200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:113838200-113842200	Weak transcription	Stomach Mucosa	stomach
7	chr2:113838600-113842000	Weak transcription	NHEK	skin
8	chr2:113838800-113842000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links