Variant report

Variant	rs12520494
Chromosome Location	chr5:54116750-54116751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10036257	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10036606	0.98[ASN][1000 genomes]
rs10039924	0.87[ASN][1000 genomes]
rs10042288	0.98[ASN][1000 genomes]
rs10042394	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10042495	0.98[ASN][1000 genomes]
rs10043408	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10044938	0.93[AFR][1000 genomes]
rs10045175	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10045765	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10045790	0.87[ASN][1000 genomes]
rs10050561	0.86[ASN][1000 genomes]
rs10053168	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10057871	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10058571	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10058862	0.98[ASN][1000 genomes]
rs10058905	0.82[AFR][1000 genomes]
rs10061958	0.81[ASN][1000 genomes]
rs10066294	0.97[ASN][1000 genomes]
rs10066622	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10066683	0.83[AFR][1000 genomes]
rs10068073	0.86[ASN][1000 genomes]
rs10071183	0.87[ASN][1000 genomes]
rs10073662	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10073721	0.87[ASN][1000 genomes]
rs10434559	0.86[ASN][1000 genomes]
rs10461588	0.95[ASN][1000 genomes]
rs10471923	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1073709	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10737956	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10805463	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10805468	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10805469	0.97[ASN][1000 genomes]
rs10940427	0.93[ASN][1000 genomes]
rs10940428	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11950757	0.85[ASN][1000 genomes]
rs11952681	0.94[ASN][1000 genomes]
rs11959080	0.86[ASN][1000 genomes]
rs12514244	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12515327	0.97[ASN][1000 genomes]
rs12522199	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13155441	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13161386	0.94[ASN][1000 genomes]
rs13161718	0.94[ASN][1000 genomes]
rs13167527	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13171964	0.94[ASN][1000 genomes]
rs13173669	0.98[ASN][1000 genomes]
rs13180287	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13186455	0.84[AFR][1000 genomes]
rs13186826	0.98[ASN][1000 genomes]
rs35922886	0.90[AFR][1000 genomes]
rs4074332	0.91[JPT][hapmap]
rs4242044	0.87[ASN][1000 genomes]
rs4242045	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4242046	0.97[ASN][1000 genomes]
rs4242047	0.97[ASN][1000 genomes]
rs4242048	0.94[ASN][1000 genomes]
rs4282277	0.86[ASN][1000 genomes]
rs4289528	0.97[ASN][1000 genomes]
rs4290968	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4292417	0.80[ASN][1000 genomes]
rs4298212	0.86[ASN][1000 genomes]
rs4320207	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4336310	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4336311	0.94[ASN][1000 genomes]
rs4356994	0.87[ASN][1000 genomes]
rs4362906	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4437335	0.94[ASN][1000 genomes]
rs4451013	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4451014	0.94[ASN][1000 genomes]
rs4457032	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4464652	0.85[AFR][1000 genomes]
rs4498213	0.86[ASN][1000 genomes]
rs4505913	0.86[ASN][1000 genomes]
rs4519880	0.98[ASN][1000 genomes]
rs4527555	0.98[ASN][1000 genomes]
rs4527556	0.98[ASN][1000 genomes]
rs4582235	0.94[ASN][1000 genomes]
rs4591702	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4610422	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4645296	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4865586	0.91[JPT][hapmap]
rs4865870	0.86[ASN][1000 genomes]
rs4865872	0.87[ASN][1000 genomes]
rs4865873	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4865874	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4865875	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4865876	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4865877	0.94[ASN][1000 genomes]
rs59664922	0.81[ASN][1000 genomes]
rs62355005	0.80[AFR][1000 genomes]
rs6450248	0.81[ASN][1000 genomes]
rs6450251	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6450252	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6450253	0.98[ASN][1000 genomes]
rs6860729	0.86[ASN][1000 genomes]
rs6860824	0.91[JPT][hapmap]
rs6863705	0.90[JPT][hapmap]
rs6867867	0.87[ASN][1000 genomes]
rs6887578	0.94[ASN][1000 genomes]
rs6892315	0.87[ASN][1000 genomes]
rs6899052	0.95[ASN][1000 genomes]
rs73126822	0.81[ASN][1000 genomes]
rs73126828	0.81[ASN][1000 genomes]
rs73126830	0.81[ASN][1000 genomes]
rs7446423	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7446869	0.94[ASN][1000 genomes]
rs7726707	0.81[ASN][1000 genomes]
rs7728303	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7728418	0.81[ASN][1000 genomes]
rs7731103	0.96[ASN][1000 genomes]
rs9292072	0.81[ASN][1000 genomes]
rs9292073	0.87[ASN][1000 genomes]
rs9292074	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9687636	0.98[ASN][1000 genomes]
rs9968754	0.97[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	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54109400-54117800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:54115400-54118000	Enhancers	HUVEC	blood vessel
3	chr5:54115400-54121200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:54115800-54117000	Enhancers	Osteobl	bone
5	chr5:54115800-54119800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:54116000-54116800	Enhancers	NH-A	brain
7	chr5:54116000-54117000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:54116000-54117000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:54116000-54117200	Enhancers	Aorta	Aorta
10	chr5:54116000-54117800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:54116000-54118000	Enhancers	Fetal Heart	heart
12	chr5:54116000-54121000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:54116400-54117200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:54116600-54117000	Enhancers	NHLF	lung
15	chr5:54116600-54117200	Enhancers	HSMMtube	muscle
16	chr5:54116600-54119200	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links