Variant report

Variant	rs9819246
Chromosome Location	chr3:100264716-100264717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10936221	0.93[CHB][hapmap]
rs11706258	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710281	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11713258	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715555	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11923487	0.84[ASN][1000 genomes]
rs12629511	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12630904	0.82[ASN][1000 genomes]
rs12634314	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12634317	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12635025	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12635026	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12636452	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12639465	0.93[CHB][hapmap];0.80[JPT][hapmap]
rs13093980	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13320223	0.82[ASN][1000 genomes]
rs28722928	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3924054	0.80[CHB][hapmap]
rs4075020	0.86[CHB][hapmap]
rs4077302	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4129205	0.87[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4928048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928049	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4928063	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928064	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928065	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4928111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4928112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55764247	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55789829	0.95[ASN][1000 genomes]
rs56736439	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57075146	0.83[ASN][1000 genomes]
rs57404153	0.84[ASN][1000 genomes]
rs57671998	0.83[ASN][1000 genomes]
rs58689996	0.95[ASN][1000 genomes]
rs58740980	0.82[ASN][1000 genomes]
rs58789183	0.98[ASN][1000 genomes]
rs59281247	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60255102	0.81[ASN][1000 genomes]
rs60375749	0.83[ASN][1000 genomes]
rs60511852	0.95[ASN][1000 genomes]
rs61403861	0.83[ASN][1000 genomes]
rs62274560	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274561	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62274575	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278361	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441300	0.89[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap]
rs6441308	0.93[CHB][hapmap]
rs6441316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441317	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441318	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441321	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441329	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66512877	0.82[ASN][1000 genomes]
rs66627492	0.81[ASN][1000 genomes]
rs66644999	0.82[ASN][1000 genomes]
rs66747627	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66828943	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67014477	0.82[ASN][1000 genomes]
rs67348505	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763638	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6767089	0.82[ASN][1000 genomes]
rs6777810	0.93[CHB][hapmap]
rs6780654	0.93[CHB][hapmap]
rs6792014	0.93[CHB][hapmap]
rs6796541	0.83[ASN][1000 genomes]
rs6799879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6799882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6799992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68019545	0.82[ASN][1000 genomes]
rs6802787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6803109	0.83[ASN][1000 genomes]
rs6805186	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6807804	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72929220	0.83[ASN][1000 genomes]
rs73141201	0.82[ASN][1000 genomes]
rs7426462	0.84[ASN][1000 genomes]
rs7426815	0.81[CHB][hapmap]
rs7427360	0.84[ASN][1000 genomes]
rs7429277	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7429392	0.86[CHB][hapmap]
rs7429915	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs7431846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7432710	0.88[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs7433589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7433875	0.84[ASN][1000 genomes]
rs7611100	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7617909	0.84[ASN][1000 genomes]
rs7618030	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618159	0.80[ASN][1000 genomes]
rs7622658	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7625717	0.83[ASN][1000 genomes]
rs7631877	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7644235	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7645690	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7645700	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647492	0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7647499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7650265	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653126	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653196	0.84[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap]
rs9809934	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9814643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823159	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9825818	0.84[ASN][1000 genomes]
rs9831654	0.82[ASN][1000 genomes]
rs9842488	0.82[ASN][1000 genomes]
rs9843498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843647	0.82[ASN][1000 genomes]
rs9843654	0.82[ASN][1000 genomes]
rs9845649	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9855549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857812	0.81[ASN][1000 genomes]
rs9865411	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9865776	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9870803	0.83[ASN][1000 genomes]
rs9880036	0.93[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9881835	0.82[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9819246	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100238000-100265400	Weak transcription	HSMMtube	muscle
2	chr3:100241000-100299800	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:100242400-100265000	Weak transcription	HepG2	liver
4	chr3:100242400-100268000	Weak transcription	Ovary	ovary
5	chr3:100244800-100267000	Weak transcription	HSMM	muscle
6	chr3:100253800-100289000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:100253800-100289000	Weak transcription	Aorta	Aorta
8	chr3:100254000-100269400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:100255000-100274800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:100255600-100266600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:100255800-100267600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:100256800-100266800	Weak transcription	Fetal Stomach	stomach
13	chr3:100256800-100268200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:100257400-100265200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:100257600-100267200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:100261000-100267000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:100261800-100277000	Weak transcription	Fetal Lung	lung
18	chr3:100263400-100265000	Weak transcription	NHEK	skin
19	chr3:100264200-100264800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:100264200-100265400	Enhancers	HMEC	breast
21	chr3:100264200-100265600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:100264200-100265800	Enhancers	Hela-S3	cervix
23	chr3:100264400-100265600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links