Variant report

Variant	rs6799992
Chromosome Location	chr3:100255282-100255283
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	chr3:100241152..100243622-chr3:100252905..100255777,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10936221	0.94[CHB][hapmap]
rs11706258	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710281	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11713258	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11715555	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11923487	0.83[ASN][1000 genomes]
rs12630904	0.81[ASN][1000 genomes]
rs12634314	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12634317	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12635025	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12635026	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12636452	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12639465	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs13093980	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13320223	0.81[ASN][1000 genomes]
rs1676340	0.82[YRI][hapmap]
rs28722928	0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3924054	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs4075020	0.88[CHB][hapmap]
rs4077302	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4129205	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4928048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928049	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4928063	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928064	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928065	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928110	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4928111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4928112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55764247	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55789829	0.97[ASN][1000 genomes]
rs56736439	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57075146	0.82[ASN][1000 genomes]
rs57404153	0.83[ASN][1000 genomes]
rs57671998	0.82[ASN][1000 genomes]
rs58689996	0.97[ASN][1000 genomes]
rs58740980	0.80[ASN][1000 genomes]
rs58789183	0.96[ASN][1000 genomes]
rs59281247	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60375749	0.82[ASN][1000 genomes]
rs60511852	0.97[ASN][1000 genomes]
rs61403861	0.82[ASN][1000 genomes]
rs62274560	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274561	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274575	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62278361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441300	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs6441308	0.94[CHB][hapmap]
rs6441316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441317	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441318	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441321	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441328	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6441329	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66512877	0.81[ASN][1000 genomes]
rs66644999	0.81[ASN][1000 genomes]
rs66747627	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66828943	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67014477	0.81[ASN][1000 genomes]
rs67348505	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6763638	0.83[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6767089	0.81[ASN][1000 genomes]
rs6777810	0.94[CHB][hapmap]
rs6780654	0.94[CHB][hapmap]
rs6792014	0.94[CHB][hapmap]
rs6796541	0.82[ASN][1000 genomes]
rs6799879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68019545	0.81[ASN][1000 genomes]
rs6802787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803109	0.82[ASN][1000 genomes]
rs6805186	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6807804	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6808426	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]
rs72929220	0.82[ASN][1000 genomes]
rs73141201	0.81[ASN][1000 genomes]
rs7426462	0.83[ASN][1000 genomes]
rs7426815	0.89[CHB][hapmap]
rs7427360	0.83[ASN][1000 genomes]
rs7429277	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7429392	0.89[CHB][hapmap]
rs7429915	0.83[CHB][hapmap];0.82[GIH][hapmap];0.81[ASN][1000 genomes]
rs7431846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7432710	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7433589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433875	0.83[ASN][1000 genomes]
rs7611100	0.89[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs7617909	0.83[ASN][1000 genomes]
rs7618030	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7622658	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7625717	0.82[ASN][1000 genomes]
rs7631877	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7644235	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645690	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7645700	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7647492	0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7647499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7650265	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653126	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653196	0.80[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs9809934	0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs9814643	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819246	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]
rs9820745	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9823159	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9825818	0.83[ASN][1000 genomes]
rs9831654	0.81[ASN][1000 genomes]
rs9842488	0.81[ASN][1000 genomes]
rs9843498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9843647	0.81[ASN][1000 genomes]
rs9843654	0.81[ASN][1000 genomes]
rs9845649	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9855549	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]
rs9865411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9865776	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9870803	0.82[ASN][1000 genomes]
rs9880036	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9881835	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6799992	TMEM45A	cis	parietal	SCAN
rs6799992	TFG	cis	multi-tissue	Pritchard
rs6799992	OR5K4	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr3:100244600-100261400	Weak transcription	Fetal Lung	lung
6	chr3:100244800-100255400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:100244800-100257800	Weak transcription	Spleen	Spleen
8	chr3:100244800-100267000	Weak transcription	HSMM	muscle
9	chr3:100245400-100255800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:100251000-100257400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:100251400-100255600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:100251800-100257000	Enhancers	Hela-S3	cervix
13	chr3:100253200-100256200	Enhancers	Liver	Liver
14	chr3:100253200-100257400	Enhancers	HMEC	breast
15	chr3:100253800-100289000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:100253800-100289000	Weak transcription	Aorta	Aorta
17	chr3:100254000-100255800	Weak transcription	Fetal Stomach	stomach
18	chr3:100254000-100269400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:100254200-100257400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr3:100254400-100255400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:100254600-100255400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:100254600-100255600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:100254600-100255800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:100254600-100255800	Enhancers	NHEK	skin
25	chr3:100254800-100255400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:100255000-100255400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:100255000-100256600	Enhancers	Pancreas	Pancrea
28	chr3:100255000-100274800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:100255200-100256400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:100255200-100258600	Weak transcription	Muscle Satellite Cultured Cells	--

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