Variant report

Variant	rs12639465
Chromosome Location	chr3:100225478-100225479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100222273..100224210-chr3:100224427..100226552,2	MCF-7	breast:
2	chr3:100223819..100226546-chr3:100278387..100280619,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10936221	0.89[CHB][hapmap]
rs11719592	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs11920006	0.81[JPT][hapmap]
rs11923942	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11927516	1.00[CEU][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12631075	0.89[CEU][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs12634317	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs12634371	0.85[EUR][1000 genomes]
rs12636452	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap]
rs12636805	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28722928	0.83[CHB][hapmap]
rs4075020	0.94[CHB][hapmap]
rs4077302	0.83[CHB][hapmap]
rs4132537	0.85[JPT][hapmap]
rs4928048	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs4928049	0.83[CHB][hapmap]
rs4928097	0.89[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs4928098	0.81[JPT][hapmap]
rs4928110	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes]
rs4928111	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4928112	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs55789829	0.86[AMR][1000 genomes]
rs56402168	0.91[ASN][1000 genomes]
rs56779007	0.94[ASN][1000 genomes]
rs57018910	0.89[EUR][1000 genomes]
rs59299896	0.89[EUR][1000 genomes]
rs60071944	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60272820	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61636409	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62276517	0.86[EUR][1000 genomes]
rs62276520	0.89[EUR][1000 genomes]
rs62276521	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62276522	0.89[EUR][1000 genomes]
rs62276523	0.86[EUR][1000 genomes]
rs62276526	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62276556	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62276559	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441300	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6441308	0.89[CHB][hapmap]
rs6441316	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6441328	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6441329	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs66791174	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67600559	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6763079	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6763178	0.92[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67774605	0.89[EUR][1000 genomes]
rs6777810	0.89[CHB][hapmap]
rs6780654	0.89[CHB][hapmap]
rs6792014	0.89[CHB][hapmap]
rs6798264	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6799879	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6799882	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6799992	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6802787	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6807804	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6808426	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs73152126	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7426815	0.83[CHB][hapmap]
rs7429072	0.89[EUR][1000 genomes]
rs7429277	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7429392	0.94[CHB][hapmap]
rs7429604	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7430698	0.89[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7430715	0.89[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7431846	0.89[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7433589	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7611100	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs7619507	0.81[JPT][hapmap]
rs7622658	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7631877	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7645690	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs7645700	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7647499	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7650523	0.94[ASN][1000 genomes]
rs7653196	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9809934	0.83[CHB][hapmap]
rs9810780	0.83[ASN][1000 genomes]
rs9819246	0.93[CHB][hapmap];0.80[JPT][hapmap]
rs9823159	0.83[CHB][hapmap]
rs9843498	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs9851429	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9855549	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs9865411	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs9865776	0.83[CHB][hapmap]
rs9880036	0.81[CHB][hapmap];0.84[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	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12639465	OR5K4	cis	cerebellum	SCAN
rs12639465	TMEM45A	cis	parietal	SCAN
rs12639465	TMEM45A	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100216200-100229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:100220400-100226800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:100224200-100226000	Enhancers	Liver	Liver
4	chr3:100224600-100225600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:100224800-100225600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:100224800-100225800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:100224800-100225800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:100224800-100225800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:100224800-100225800	Enhancers	Osteobl	bone
10	chr3:100224800-100226600	Weak transcription	Pancreas	Pancrea
11	chr3:100224800-100226800	Weak transcription	Aorta	Aorta
12	chr3:100225000-100225800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:100225400-100225800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:100225400-100226000	Active TSS	Fetal Brain Male	brain
15	chr3:100225400-100226800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:100225400-100236800	Weak transcription	Placenta Amnion	Placenta Amnion

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