Variant report

Variant	rs12486955
Chromosome Location	chr3:157036787-157036788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10755111	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs10936077	0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10936079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486155	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12494423	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12636252	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1392798	0.91[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1403105	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1500921	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1500923	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1522393	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546260	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1566521	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1581413	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2321743	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs34263112	0.99[ASN][1000 genomes]
rs4680353	0.91[MEX][hapmap];0.83[TSI][hapmap]
rs55734537	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62278578	0.83[ASN][1000 genomes]
rs62278580	0.82[ASN][1000 genomes]
rs62281378	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73156724	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73156728	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7636413	0.87[MEX][hapmap]
rs7642909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs991083	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877687	chr3:156924793-157044184	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12486955	SSR3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157015600-157048400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:157030600-157047000	Weak transcription	Osteobl	bone
3	chr3:157031400-157037400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:157031800-157039200	Weak transcription	HUVEC	blood vessel
5	chr3:157035400-157036800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:157035400-157036800	Enhancers	A549	lung
7	chr3:157035600-157036800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:157036000-157047800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:157036200-157039000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:157036200-157040400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:157036400-157036800	Enhancers	Stomach Mucosa	stomach
12	chr3:157036600-157037200	Enhancers	Small Intestine	intestine

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