Variant report

Variant	rs10090819
Chromosome Location	chr8:49628125-49628126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:49616836..49619308-chr8:49627377..49629185,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10092718	0.81[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10097910	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10101066	0.85[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10111821	0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1074382	0.85[CHB][hapmap]
rs10808720	0.85[CHB][hapmap]
rs10957199	0.81[CHB][hapmap]
rs1126259	0.85[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.86[MKK][hapmap];0.84[ASN][1000 genomes]
rs11785748	0.87[ASN][1000 genomes]
rs12155607	0.85[CHB][hapmap];0.89[CHD][hapmap];0.87[ASN][1000 genomes]
rs12548278	0.83[JPT][hapmap]
rs12550270	0.81[ASN][1000 genomes]
rs13251991	0.85[CHB][hapmap]
rs13276316	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1482261	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1482262	0.85[CHB][hapmap]
rs16938731	0.81[EUR][1000 genomes]
rs1871889	0.85[CHB][hapmap]
rs2384970	0.82[ASN][1000 genomes]
rs2891648	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35243529	0.82[ASN][1000 genomes]
rs4873285	0.85[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4873288	0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs55923266	0.82[ASN][1000 genomes]
rs6984858	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6990865	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7835152	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900237	0.85[CHB][hapmap]
rs900238	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs9298058	0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs9332436	0.81[CHB][hapmap]
rs966703	0.85[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.86[MKK][hapmap];0.87[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10090819	EFCAB1	cis	cerebellum	SCAN
rs10090819	EFCAB1	cis	parietal	SCAN
rs10090819	C8orf22	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49621600-49628600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:49627000-49630600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:49627000-49647200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr8:49627800-49647400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr8:49628000-49628400	ZNF genes & repeats	Fetal Lung	lung
6	chr8:49628000-49629000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr8:49628000-49629000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr8:49628000-49629000	ZNF genes & repeats	Ovary	ovary
9	chr8:49628000-49629200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:49628000-49629400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links