Variant report

Variant	rs6441308
Chromosome Location	chr3:100242358-100242359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100240678..100242912-chr3:100244907..100246984,2	MCF-7	breast:
2	chr3:100241152..100243622-chr3:100252905..100255777,2	MCF-7	breast:
3	chr3:100234281..100237068-chr3:100240897..100243194,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10936221	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs11719592	0.94[CHB][hapmap]
rs12634317	0.94[CHB][hapmap]
rs12636452	0.94[CHB][hapmap]
rs12639465	0.89[CHB][hapmap]
rs28722928	0.83[CHB][hapmap]
rs4073343	0.98[ASN][1000 genomes]
rs4075020	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4077302	0.83[CHB][hapmap]
rs4928048	0.94[CHB][hapmap]
rs4928049	0.83[CHB][hapmap]
rs4928110	0.94[CHB][hapmap];0.82[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs4928111	0.94[CHB][hapmap]
rs4928112	0.94[CHB][hapmap]
rs55789829	0.84[AFR][1000 genomes]
rs60272820	0.86[AFR][1000 genomes]
rs62276556	0.93[AFR][1000 genomes]
rs6441300	0.89[CHB][hapmap]
rs6441316	0.94[CHB][hapmap]
rs6441328	0.94[CHB][hapmap]
rs6441329	0.94[CHB][hapmap]
rs6777810	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6780654	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6792014	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6799879	0.94[CHB][hapmap]
rs6799882	0.94[CHB][hapmap]
rs6799992	0.94[CHB][hapmap]
rs6802787	0.94[CHB][hapmap]
rs6807804	0.94[CHB][hapmap]
rs6808426	0.94[CHB][hapmap]
rs7426815	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7429277	0.94[CHB][hapmap]
rs7429392	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7431846	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs7433589	0.94[CHB][hapmap]
rs7611100	0.84[CHB][hapmap]
rs7622658	0.94[CHB][hapmap]
rs7631877	0.94[CHB][hapmap]
rs7645690	0.94[CHB][hapmap]
rs7645700	0.94[CHB][hapmap]
rs7647499	1.00[CHB][hapmap]
rs7653196	0.89[CHB][hapmap]
rs9809934	0.83[CHB][hapmap]
rs9819246	0.93[CHB][hapmap]
rs9823159	0.83[CHB][hapmap]
rs9843498	0.94[CHB][hapmap]
rs9855549	0.94[CHB][hapmap]
rs9865411	0.94[CHB][hapmap]
rs9865776	0.83[CHB][hapmap]
rs9880036	0.82[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
rs6441308	TMEM45A	cis	Whole Blood	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100235800-100244800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:100236400-100242600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:100237600-100244200	Weak transcription	NH-A	brain
4	chr3:100238000-100244400	Weak transcription	Adipose Nuclei	Adipose
5	chr3:100238000-100244400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:100238000-100252600	Weak transcription	Fetal Intestine Small	intestine
7	chr3:100238000-100265400	Weak transcription	HSMMtube	muscle
8	chr3:100238200-100244400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:100238200-100244400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:100238200-100244400	Weak transcription	HSMM	muscle
11	chr3:100238400-100244200	Weak transcription	NHDF-Ad	bronchial
12	chr3:100238800-100243800	Weak transcription	HMEC	breast
13	chr3:100239000-100244200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:100239000-100244600	Weak transcription	Spleen	Spleen
15	chr3:100239200-100243200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:100239200-100243200	Strong transcription	Fetal Lung	lung
17	chr3:100239200-100244800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr3:100239400-100242400	Strong transcription	Ovary	ovary
19	chr3:100239400-100245000	Strong transcription	Fetal Stomach	stomach
20	chr3:100239400-100245200	Strong transcription	Aorta	Aorta
21	chr3:100239600-100242800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:100240600-100244400	Weak transcription	Pancreas	Pancrea
23	chr3:100240800-100242800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:100240800-100244400	Weak transcription	Placenta	Placenta
25	chr3:100241000-100299800	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:100241200-100242400	Enhancers	Liver	Liver
27	chr3:100241200-100243800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:100241200-100243800	Weak transcription	NHEK	skin
29	chr3:100241200-100251800	Weak transcription	Hela-S3	cervix
30	chr3:100241400-100244400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:100241600-100242400	Strong transcription	HepG2	liver
32	chr3:100241600-100244800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:100241800-100242800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:100241800-100244600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:100242000-100253200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:100242200-100243600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:100242200-100243800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:100242200-100244400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:100242200-100244400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:100242200-100244600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:100242200-100246400	Weak transcription	Fetal Muscle Trunk	muscle

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