Variant report

Variant	rs6682503
Chromosome Location	chr1:86527492-86527493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10518362	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11161727	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12057842	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12077017	1.00[ASN][1000 genomes]
rs12354099	1.00[ASN][1000 genomes]
rs12354100	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12729890	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12750946	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1359419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1698742	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1698743	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1698744	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17405880	1.00[ASN][1000 genomes]
rs17405900	1.00[ASN][1000 genomes]
rs17406104	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs17406138	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17406173	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17414498	1.00[ASN][1000 genomes]
rs17414519	1.00[ASN][1000 genomes]
rs17414568	1.00[ASN][1000 genomes]
rs17414617	1.00[ASN][1000 genomes]
rs2134411	0.82[CHB][hapmap]
rs34848727	1.00[ASN][1000 genomes]
rs471070	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs477562	0.90[ASN][1000 genomes]
rs489267	1.00[ASN][1000 genomes]
rs4912442	1.00[ASN][1000 genomes]
rs4912443	1.00[ASN][1000 genomes]
rs4912459	1.00[ASN][1000 genomes]
rs500756	1.00[ASN][1000 genomes]
rs511363	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs511732	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs516799	1.00[ASN][1000 genomes]
rs518538	1.00[ASN][1000 genomes]
rs519361	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs521253	1.00[ASN][1000 genomes]
rs532684	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs538256	0.82[CHD][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs547023	1.00[ASN][1000 genomes]
rs551670	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55766419	1.00[ASN][1000 genomes]
rs56040491	1.00[ASN][1000 genomes]
rs56229462	1.00[ASN][1000 genomes]
rs56392000	1.00[ASN][1000 genomes]
rs567565	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs567617	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs569409	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs570172	1.00[ASN][1000 genomes]
rs574780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs580540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs582517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs584895	0.95[ASN][1000 genomes]
rs586240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs586629	0.97[ASN][1000 genomes]
rs599761	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs612256	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs615805	1.00[ASN][1000 genomes]
rs616281	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs617652	0.90[ASN][1000 genomes]
rs631512	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs632295	1.00[ASN][1000 genomes]
rs632697	1.00[ASN][1000 genomes]
rs634946	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs635391	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs635397	1.00[ASN][1000 genomes]
rs635713	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs636210	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs647380	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs650216	1.00[ASN][1000 genomes]
rs663463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs663901	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs664099	1.00[ASN][1000 genomes]
rs664412	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6658643	1.00[ASN][1000 genomes]
rs6703328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs679256	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs680179	0.95[ASN][1000 genomes]
rs72716130	1.00[ASN][1000 genomes]
rs72958291	1.00[ASN][1000 genomes]
rs7411998	1.00[ASN][1000 genomes]

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	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525678	chr1:86487914-86549498	Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6682503	LOC339524	cis	parietal	SCAN
rs6682503	LOC339524	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86523000-86533800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:86526800-86528600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:86527000-86527600	Enhancers	GM12878-XiMat	blood
4	chr1:86527000-86528600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:86527000-86528800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:86527000-86528800	Enhancers	Osteobl	bone
7	chr1:86527200-86527600	Enhancers	Fetal Lung	lung
8	chr1:86527200-86527800	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr1:86527200-86528000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:86527200-86528600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:86527200-86528600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:86527400-86527800	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links