Variant report

Variant	rs262534
Chromosome Location	chr2:63906375-63906376
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63905199..63906853-chr2:64102018..64104600,2	MCF-7	breast:
2	chr2:63902199..63904548-chr2:63905290..63907051,2	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10168545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1023820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1031221	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10469944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10469945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1082363	0.90[ASN][1000 genomes]
rs10865338	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10865339	0.90[ASN][1000 genomes]
rs11125977	1.00[CHB][hapmap]
rs112194	0.90[ASN][1000 genomes]
rs11693909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12105140	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12473342	1.00[CHB][hapmap]
rs1255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12713496	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1348803	1.00[ASN][1000 genomes]
rs1348806	1.00[ASN][1000 genomes]
rs1374308	1.00[ASN][1000 genomes]
rs1446563	1.00[ASN][1000 genomes]
rs1446564	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1446565	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1446569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1550860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs166384	0.90[ASN][1000 genomes]
rs166385	1.00[ASN][1000 genomes]
rs17028100	1.00[CHB][hapmap]
rs171901	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs171902	1.00[ASN][1000 genomes]
rs174485	0.90[ASN][1000 genomes]
rs17619598	1.00[CHB][hapmap]
rs17619855	1.00[CHB][hapmap]
rs185499	0.90[ASN][1000 genomes]
rs1867847	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1867849	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs187801	0.90[ASN][1000 genomes]
rs1900303	1.00[ASN][1000 genomes]
rs196123	0.90[ASN][1000 genomes]
rs196124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs196125	0.90[ASN][1000 genomes]
rs2028887	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap]
rs2121350	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2121351	0.90[ASN][1000 genomes]
rs2121353	1.00[ASN][1000 genomes]
rs2166494	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2305157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2422007	1.00[JPT][hapmap]
rs2422011	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2592386	1.00[ASN][1000 genomes]
rs2592387	1.00[ASN][1000 genomes]
rs2592388	1.00[ASN][1000 genomes]
rs2604613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2604614	1.00[ASN][1000 genomes]
rs2604615	1.00[ASN][1000 genomes]
rs2604617	0.83[ASN][1000 genomes]
rs262470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs262472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs262473	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs262475	0.90[ASN][1000 genomes]
rs262476	0.90[ASN][1000 genomes]
rs262477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs262478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs262479	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs262480	0.90[ASN][1000 genomes]
rs262481	0.90[ASN][1000 genomes]
rs262482	0.90[ASN][1000 genomes]
rs262483	0.90[ASN][1000 genomes]
rs262484	0.90[ASN][1000 genomes]
rs262485	0.90[ASN][1000 genomes]
rs262487	0.90[ASN][1000 genomes]
rs262488	0.90[ASN][1000 genomes]
rs262490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs262491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs262492	0.90[ASN][1000 genomes]
rs262493	0.90[ASN][1000 genomes]
rs262494	0.90[ASN][1000 genomes]
rs262495	0.90[ASN][1000 genomes]
rs262501	0.90[ASN][1000 genomes]
rs262502	0.90[ASN][1000 genomes]
rs262503	0.90[ASN][1000 genomes]
rs262504	0.90[ASN][1000 genomes]
rs262505	0.90[ASN][1000 genomes]
rs262506	0.90[ASN][1000 genomes]
rs262507	0.90[ASN][1000 genomes]
rs262508	1.00[ASN][1000 genomes]
rs262509	1.00[ASN][1000 genomes]
rs262510	0.83[ASN][1000 genomes]
rs262511	1.00[ASN][1000 genomes]
rs262512	1.00[ASN][1000 genomes]
rs262513	0.83[ASN][1000 genomes]
rs262514	1.00[ASN][1000 genomes]
rs262515	1.00[ASN][1000 genomes]
rs262516	1.00[ASN][1000 genomes]
rs262517	1.00[ASN][1000 genomes]
rs262518	1.00[ASN][1000 genomes]
rs262519	1.00[ASN][1000 genomes]
rs262520	1.00[ASN][1000 genomes]
rs262521	1.00[ASN][1000 genomes]
rs262523	1.00[ASN][1000 genomes]
rs262524	0.83[ASN][1000 genomes]
rs262525	1.00[ASN][1000 genomes]
rs262526	1.00[ASN][1000 genomes]
rs262527	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs262528	1.00[ASN][1000 genomes]
rs262529	1.00[ASN][1000 genomes]
rs262530	1.00[ASN][1000 genomes]
rs262531	1.00[ASN][1000 genomes]
rs262533	1.00[ASN][1000 genomes]
rs262535	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262536	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs262537	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs262538	1.00[ASN][1000 genomes]
rs262539	1.00[ASN][1000 genomes]
rs4671065	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4671069	0.90[ASN][1000 genomes]
rs4671515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6546018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6546019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6708804	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6717031	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6730863	1.00[CHB][hapmap]
rs6738190	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7570031	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7576316	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7580520	1.00[JPT][hapmap]
rs7584404	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7606045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs9309355	1.00[CHB][hapmap]
rs959195	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs964880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs964903	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9789351	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs989527	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv834242	chr2:63891249-64045617	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs262534	WDPCP	cis	Adipose Subcutaneous	GTEx
rs262534	MDH1	cis	cerebellum	SCAN
rs262534	MDH1	cis	Adipose Subcutaneous	GTEx
rs262534	LOC51057	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63896400-63907200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:63896400-63911400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:63901000-63907000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:63901400-63907400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:63904000-63906400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:63905600-63909200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:63905800-63907200	Enhancers	NHEK	skin
8	chr2:63905800-63907400	Weak transcription	Adipose Nuclei	Adipose
9	chr2:63905800-63909200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:63906200-63906600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr2:63906200-63907000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:63906200-63907200	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links