Variant report

Variant	rs58608513
Chromosome Location	chr3:79000818-79000819
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10514741	0.81[AFR][1000 genomes]
rs13317939	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321050	0.90[AFR][1000 genomes]
rs13321792	0.90[AFR][1000 genomes]
rs13321973	0.90[AFR][1000 genomes]
rs13322089	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325291	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325521	0.90[AFR][1000 genomes]
rs1480685	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1480686	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17016573	0.92[EUR][1000 genomes]
rs17016593	0.92[EUR][1000 genomes]
rs17016641	0.89[AFR][1000 genomes]
rs17016648	0.84[AFR][1000 genomes]
rs2271575	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28412538	0.85[AFR][1000 genomes]
rs28431826	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564735	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28611062	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28667917	0.92[AFR][1000 genomes]
rs57432814	0.82[AFR][1000 genomes]
rs59931439	0.92[EUR][1000 genomes]
rs72904273	0.92[EUR][1000 genomes]
rs72904277	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72906141	0.92[EUR][1000 genomes]
rs72906176	0.90[AFR][1000 genomes]
rs72910206	0.91[AFR][1000 genomes]
rs72910208	0.89[AFR][1000 genomes]
rs72910211	0.83[AFR][1000 genomes]
rs72910224	0.90[AFR][1000 genomes]
rs9631526	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809330	0.89[AFR][1000 genomes]
rs9818387	0.92[AFR][1000 genomes]
rs9822620	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829918	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9832632	0.81[AFR][1000 genomes]
rs9835586	1.00[EUR][1000 genomes]
rs9836486	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9838831	0.88[AFR][1000 genomes]
rs9839144	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839572	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9842144	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853126	0.83[AFR][1000 genomes]
rs9858080	0.90[AFR][1000 genomes]
rs9868575	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870336	0.84[AFR][1000 genomes]
rs9871957	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876637	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9879944	0.81[AFR][1000 genomes]
rs9880690	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78982400-79001800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:78988000-79002400	Weak transcription	Aorta	Aorta
3	chr3:79000600-79001000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:79000600-79001000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:79000600-79001000	Enhancers	Brain Substantia Nigra	brain
6	chr3:79000600-79001000	Flanking Active TSS	Colon Smooth Muscle	Colon
7	chr3:79000600-79001000	Enhancers	Fetal Kidney	kidney
8	chr3:79000600-79001000	Enhancers	Fetal Stomach	stomach
9	chr3:79000600-79001000	Enhancers	Ovary	ovary
10	chr3:79000600-79001000	Enhancers	Rectal Smooth Muscle	rectum
11	chr3:79000600-79001000	Enhancers	A549	lung
12	chr3:79000600-79001000	Enhancers	HepG2	liver
13	chr3:79000800-79001600	Weak transcription	Fetal Lung	lung

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