Variant report

Variant	rs17727250
Chromosome Location	chr3:158905130-158905131
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10470473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936173	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10936175	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10936176	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs11715082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11924990	0.88[CEU][hapmap]
rs13326945	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13327211	0.90[CHB][hapmap]
rs1449020	1.00[YRI][hapmap]
rs1449021	0.85[EUR][1000 genomes]
rs2122147	0.81[EUR][1000 genomes]
rs2365483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365490	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs3924807	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679855	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680492	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4680497	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680498	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57473274	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58290749	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6791853	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap]
rs9820047	0.87[CEU][hapmap]
rs9827242	1.00[CEU][hapmap]
rs9827400	0.89[CEU][hapmap]
rs9829189	0.85[EUR][1000 genomes]
rs9834328	0.81[JPT][hapmap]
rs9839112	0.86[CEU][hapmap]
rs9840972	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9856166	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9862769	0.87[CEU][hapmap]
rs9878883	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9880642	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3426016	chr3:158676623-158979242	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv491927	chr3:158692653-158952780	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	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	chr3:158899600-158907400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:158903000-158905600	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:158903200-158906600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:158903200-158909200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:158904200-158905600	Enhancers	Adipose Nuclei	Adipose
6	chr3:158904400-158905200	Enhancers	Fetal Stomach	stomach
7	chr3:158904400-158905600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:158904600-158905200	Flanking Active TSS	Liver	Liver
9	chr3:158904600-158905600	Enhancers	Right Atrium	heart
10	chr3:158904800-158905400	Enhancers	GM12878-XiMat	blood
11	chr3:158905000-158905800	Enhancers	Stomach Mucosa	stomach
12	chr3:158905000-158907400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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