Variant report

Variant	rs7429277
Chromosome Location	chr3:100243445-100243446
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	chr3:100241152..100243622-chr3:100252905..100255777,2	MCF-7	breast:

Extended variants
information (count: 121 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10936221	0.94[CHB][hapmap]
rs11706258	0.88[ASN][1000 genomes]
rs11710281	0.88[ASN][1000 genomes]
rs11713258	0.86[ASN][1000 genomes]
rs11715555	0.86[ASN][1000 genomes]
rs11719592	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11923942	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11927516	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12631075	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12634314	0.86[ASN][1000 genomes]
rs12634317	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12634371	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12635025	0.86[ASN][1000 genomes]
rs12635026	0.86[ASN][1000 genomes]
rs12636452	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12636805	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12639465	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13093980	0.81[ASN][1000 genomes]
rs28722928	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs3924054	0.83[CHB][hapmap]
rs4075020	0.88[CHB][hapmap]
rs4077302	0.89[CHB][hapmap]
rs4129205	0.84[CHB][hapmap]
rs4132537	0.82[JPT][hapmap]
rs4928048	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4928049	0.89[CHB][hapmap]
rs4928063	0.88[ASN][1000 genomes]
rs4928064	0.86[ASN][1000 genomes]
rs4928065	0.86[ASN][1000 genomes]
rs4928097	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4928110	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4928111	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4928112	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs55764247	0.88[ASN][1000 genomes]
rs55789829	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56736439	0.88[ASN][1000 genomes]
rs57018910	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58689996	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58789183	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59281247	0.85[ASN][1000 genomes]
rs59299896	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60071944	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60272820	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60511852	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61636409	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62274560	0.88[ASN][1000 genomes]
rs62274561	0.88[ASN][1000 genomes]
rs62274575	0.86[ASN][1000 genomes]
rs62276517	0.89[EUR][1000 genomes]
rs62276520	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62276521	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62276522	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62276523	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62276526	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62276556	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62276559	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62278361	0.90[ASN][1000 genomes]
rs6441300	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs6441308	0.94[CHB][hapmap]
rs6441316	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6441317	0.89[ASN][1000 genomes]
rs6441318	0.89[ASN][1000 genomes]
rs6441321	0.82[ASN][1000 genomes]
rs6441328	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6441329	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs66747627	0.88[ASN][1000 genomes]
rs66791174	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66828943	0.88[ASN][1000 genomes]
rs67348505	0.88[ASN][1000 genomes]
rs67600559	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6763079	0.80[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6763178	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6763638	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs67774605	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6777810	0.94[CHB][hapmap]
rs6780654	0.94[CHB][hapmap]
rs6792014	0.94[CHB][hapmap]
rs6798264	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6799879	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6799882	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6799992	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6802787	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6805186	0.85[ASN][1000 genomes]
rs6807804	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6808426	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs73152126	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7426815	0.84[CHB][hapmap]
rs7429072	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7429392	0.89[CHB][hapmap]
rs7429604	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7429915	0.83[CHB][hapmap]
rs7430698	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7430715	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7431846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7432710	0.84[CHB][hapmap]
rs7433589	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7611100	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs7618030	0.87[ASN][1000 genomes]
rs7622658	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7631877	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7644235	0.85[ASN][1000 genomes]
rs7645690	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7645700	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7647492	0.83[JPT][hapmap]
rs7647499	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7650265	0.88[ASN][1000 genomes]
rs7653126	0.88[ASN][1000 genomes]
rs7653196	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs9809934	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs9814643	0.88[ASN][1000 genomes]
rs9819246	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs9820745	0.88[ASN][1000 genomes]
rs9823159	0.89[CHB][hapmap]
rs9843498	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9845649	0.86[ASN][1000 genomes]
rs9851429	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9855549	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9865411	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9865776	0.89[CHB][hapmap]
rs9880036	0.88[CHB][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7429277	TMEM45A	cis	Whole Blood	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100235800-100244800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:100237600-100244200	Weak transcription	NH-A	brain
3	chr3:100238000-100244400	Weak transcription	Adipose Nuclei	Adipose
4	chr3:100238000-100244400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:100238000-100252600	Weak transcription	Fetal Intestine Small	intestine
6	chr3:100238000-100265400	Weak transcription	HSMMtube	muscle
7	chr3:100238200-100244400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:100238200-100244400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:100238200-100244400	Weak transcription	HSMM	muscle
10	chr3:100238400-100244200	Weak transcription	NHDF-Ad	bronchial
11	chr3:100238800-100243800	Weak transcription	HMEC	breast
12	chr3:100239000-100244200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:100239000-100244600	Weak transcription	Spleen	Spleen
14	chr3:100239200-100244800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr3:100239400-100245000	Strong transcription	Fetal Stomach	stomach
16	chr3:100239400-100245200	Strong transcription	Aorta	Aorta
17	chr3:100240600-100244400	Weak transcription	Pancreas	Pancrea
18	chr3:100240800-100244400	Weak transcription	Placenta	Placenta
19	chr3:100241000-100299800	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:100241200-100243800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:100241200-100243800	Weak transcription	NHEK	skin
22	chr3:100241200-100251800	Weak transcription	Hela-S3	cervix
23	chr3:100241400-100244400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:100241600-100244800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr3:100241800-100244600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:100242000-100253200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:100242200-100243600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:100242200-100243800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:100242200-100244400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:100242200-100244400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:100242200-100244600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:100242200-100246400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:100242400-100244400	Weak transcription	Liver	Liver
34	chr3:100242400-100265000	Weak transcription	HepG2	liver
35	chr3:100242400-100268000	Weak transcription	Ovary	ovary
36	chr3:100242800-100244200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:100242800-100244400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:100243000-100243600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:100243200-100244000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:100243200-100244400	Weak transcription	Fetal Lung	lung

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