Variant report

Variant	rs12474942
Chromosome Location	chr2:190056582-190056583
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10165127	0.84[AFR][1000 genomes]
rs10165257	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10166385	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10167242	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10172607	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10173224	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10184895	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10188246	0.85[EUR][1000 genomes]
rs10755002	0.93[ASN][1000 genomes]
rs10804029	0.87[EUR][1000 genomes]
rs10931401	0.96[ASN][1000 genomes]
rs10931403	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10931405	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10931411	0.85[ASN][1000 genomes]
rs11676905	0.89[EUR][1000 genomes]
rs11901914	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12621657	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12994482	0.89[EUR][1000 genomes]
rs12999125	0.96[ASN][1000 genomes]
rs13006065	0.99[ASN][1000 genomes]
rs13015183	0.93[ASN][1000 genomes]
rs13028226	0.96[ASN][1000 genomes]
rs13031609	0.81[ASN][1000 genomes]
rs13408928	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13411992	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13413518	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1356161	0.95[ASN][1000 genomes]
rs1356166	0.97[ASN][1000 genomes]
rs1464135	0.94[ASN][1000 genomes]
rs1474000	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1515866	0.93[ASN][1000 genomes]
rs1533618	0.98[ASN][1000 genomes]
rs1546617	0.95[ASN][1000 genomes]
rs1913892	0.95[ASN][1000 genomes]
rs1973666	0.86[ASN][1000 genomes]
rs1983318	0.97[ASN][1000 genomes]
rs2351631	0.93[ASN][1000 genomes]
rs2351632	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2351633	0.93[ASN][1000 genomes]
rs2351635	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2351932	0.85[EUR][1000 genomes]
rs2683012	0.87[EUR][1000 genomes]
rs4580411	0.82[EUR][1000 genomes]
rs4667268	0.96[ASN][1000 genomes]
rs4667270	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4667271	0.98[ASN][1000 genomes]
rs4667275	0.88[ASN][1000 genomes]
rs4667280	0.82[EUR][1000 genomes]
rs6434334	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6434337	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6434340	0.82[EUR][1000 genomes]
rs6704568	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6728877	0.96[ASN][1000 genomes]
rs6732534	0.94[ASN][1000 genomes]
rs6741804	0.85[AFR][1000 genomes]
rs6761868	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7422875	0.89[EUR][1000 genomes]
rs7425383	0.89[EUR][1000 genomes]
rs7574281	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7599222	0.95[ASN][1000 genomes]
rs7603704	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9288163	0.88[AFR][1000 genomes]
rs939158	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs939160	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 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	chr2:190045800-190056600	Weak transcription	HSMM	muscle
2	chr2:190046600-190057600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:190053200-190056600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:190053400-190056600	Weak transcription	Osteobl	bone
5	chr2:190053600-190056600	Weak transcription	NHDF-Ad	bronchial
6	chr2:190053600-190056600	Weak transcription	NHLF	lung
7	chr2:190055400-190056600	Enhancers	A549	lung
8	chr2:190056200-190056800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:190056200-190057000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:190056200-190057200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:190056400-190057200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:190056400-190057200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:190056400-190057200	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links