Variant report

Variant	rs17016573
Chromosome Location	chr3:78938564-78938565
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10511125	1.00[CEU][hapmap]
rs10511126	1.00[CEU][hapmap]
rs12330873	1.00[JPT][hapmap]
rs13317939	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13322089	0.92[EUR][1000 genomes]
rs13325291	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1480685	0.92[EUR][1000 genomes]
rs162819	1.00[CEU][hapmap]
rs162873	1.00[CEU][hapmap]
rs162875	1.00[CEU][hapmap]
rs167944	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17016495	1.00[CEU][hapmap]
rs17016507	1.00[CEU][hapmap]
rs17016511	1.00[CEU][hapmap]
rs17016593	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125123	1.00[CEU][hapmap]
rs2271575	0.92[EUR][1000 genomes]
rs28431826	0.92[EUR][1000 genomes]
rs28564735	0.92[EUR][1000 genomes]
rs28611062	0.92[EUR][1000 genomes]
rs331132	1.00[CEU][hapmap]
rs331133	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs331159	1.00[CEU][hapmap]
rs333499	1.00[CEU][hapmap]
rs333501	1.00[JPT][hapmap]
rs58608513	0.92[EUR][1000 genomes]
rs59931439	1.00[EUR][1000 genomes]
rs72896421	1.00[ASN][1000 genomes]
rs72896425	1.00[ASN][1000 genomes]
rs72896429	1.00[ASN][1000 genomes]
rs72896433	1.00[ASN][1000 genomes]
rs72896439	1.00[ASN][1000 genomes]
rs72896443	1.00[ASN][1000 genomes]
rs72896444	1.00[ASN][1000 genomes]
rs72904273	1.00[EUR][1000 genomes]
rs72904277	0.92[EUR][1000 genomes]
rs72906141	1.00[EUR][1000 genomes]
rs9631526	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9822620	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9824808	1.00[MEX][hapmap]
rs9829918	0.92[EUR][1000 genomes]
rs9835586	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9836486	0.92[EUR][1000 genomes]
rs9839144	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9839572	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9842144	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9868575	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9871957	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9876637	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs9880690	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	nsv877020	chr3:78913203-78975982	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590735	chr3:78922852-78977507	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78922600-78944000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:78923000-78943800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:78927600-78943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:78930400-78938600	Weak transcription	Psoas Muscle	Psoas
5	chr3:78930400-78942200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:78930400-78944000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:78930600-78948600	Weak transcription	Fetal Lung	lung
8	chr3:78930800-78943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:78935400-78939200	Enhancers	Fetal Brain Male	brain
10	chr3:78936400-78938600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:78936400-78938800	Enhancers	Brain Angular Gyrus	brain
12	chr3:78936400-78938800	Enhancers	Brain Hippocampus Middle	brain
13	chr3:78936800-78942000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:78937000-78943800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:78937000-78946000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:78937000-78946400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:78937200-78938800	Enhancers	NHDF-Ad	bronchial
18	chr3:78937200-78938800	Enhancers	NHEK	skin
19	chr3:78937200-78939000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:78937200-78943800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:78937400-78938600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:78937400-78939200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:78937800-78938800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:78937800-78938800	Enhancers	Brain Cingulate Gyrus	brain
25	chr3:78937800-78939200	Enhancers	Fetal Brain Female	brain
26	chr3:78937800-78942200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:78937800-78943800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:78938000-78938800	Enhancers	Brain Substantia Nigra	brain
29	chr3:78938200-78938600	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr3:78938200-78938800	Enhancers	Adipose Nuclei	Adipose
31	chr3:78938200-78953400	Weak transcription	HepG2	liver
32	chr3:78938400-78938600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:78938400-78938600	Enhancers	A549	lung

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