Variant report

Variant	rs1509462
Chromosome Location	chr5:42489345-42489346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10941577	0.95[ASN][1000 genomes]
rs11738365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11739243	0.83[CHB][hapmap];0.95[ASN][1000 genomes]
rs11741390	0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs11748084	0.94[ASN][1000 genomes]
rs12514403	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515480	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12517368	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12518010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12518274	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12522222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12522421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12654986	0.82[AMR][1000 genomes]
rs13153388	0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs13166255	0.94[ASN][1000 genomes]
rs13166285	0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs13169289	0.95[ASN][1000 genomes]
rs13178282	0.94[ASN][1000 genomes]
rs13178652	0.95[ASN][1000 genomes]
rs13189275	0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs1509455	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1509456	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1509460	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1509463	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16872543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16872564	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1858136	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1876790	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1960498	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1979994	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2036745	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2089645	0.84[ASN][1000 genomes]
rs28498583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28943875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28943877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28943879	0.84[ASN][1000 genomes]
rs2940913	0.83[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs2940917	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2940918	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2940919	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2940923	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2940927	1.00[JPT][hapmap]
rs2940937	0.97[ASN][1000 genomes]
rs2940944	0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs2972392	0.95[ASN][1000 genomes]
rs2972393	0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs2972407	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2972408	1.00[JPT][hapmap]
rs2972411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2972412	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2972413	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2972418	0.82[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs2972420	0.83[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs33956936	0.95[ASN][1000 genomes]
rs34069689	1.00[EUR][1000 genomes]
rs35500216	0.97[ASN][1000 genomes]
rs4130114	0.83[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs4509029	0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs4530764	0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs4866781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4866782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4866785	1.00[EUR][1000 genomes]
rs4866788	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4866790	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4866896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4866901	1.00[AMR][1000 genomes]
rs4866919	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4866931	0.83[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs4866932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866934	0.95[ASN][1000 genomes]
rs4866935	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58179197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451621	0.92[ASN][1000 genomes]
rs6451622	0.87[ASN][1000 genomes]
rs6451624	0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs6897318	0.95[ASN][1000 genomes]
rs7705834	0.95[ASN][1000 genomes]
rs7710528	0.91[ASN][1000 genomes]
rs7721578	0.83[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs7723304	0.94[ASN][1000 genomes]
rs949559	1.00[AFR][1000 genomes];0.98[AMR][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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42481800-42491800	Weak transcription	Aorta	Aorta
2	chr5:42484800-42491200	Weak transcription	Ovary	ovary
3	chr5:42484800-42491800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:42485000-42490200	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:42485000-42490400	Weak transcription	Fetal Muscle Leg	muscle
6	chr5:42485200-42490600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:42485400-42490400	Weak transcription	Psoas Muscle	Psoas
8	chr5:42486400-42490200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:42486400-42490400	Weak transcription	Adipose Nuclei	Adipose
10	chr5:42487400-42491600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:42487400-42494600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:42488000-42489600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:42488200-42490400	Weak transcription	Fetal Heart	heart
14	chr5:42488200-42490800	Weak transcription	Fetal Lung	lung
15	chr5:42489200-42489400	Genic enhancers	Liver	Liver

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