Variant report

Variant	rs4075020
Chromosome Location	chr3:100239024-100239025
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:217362499..217364288-chr3:100238945..100241543,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197756	Chromatin interaction
ENSG00000232485	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10936221	0.93[ASW][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs11719592	0.88[CHB][hapmap]
rs12634317	0.88[CHB][hapmap]
rs12636452	0.88[CHB][hapmap]
rs12639465	0.94[CHB][hapmap]
rs4073343	0.80[ASN][1000 genomes]
rs4928048	0.88[CHB][hapmap]
rs4928110	0.88[CHB][hapmap]
rs4928111	0.88[CHB][hapmap]
rs4928112	0.88[CHB][hapmap]
rs62276559	0.92[AFR][1000 genomes]
rs6441300	0.94[CHB][hapmap]
rs6441308	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]
rs6441316	0.88[CHB][hapmap]
rs6441328	0.88[CHB][hapmap]
rs6441329	0.88[CHB][hapmap]
rs6777810	0.93[ASW][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap]
rs6780654	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes]
rs6792014	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes]
rs6799879	0.88[CHB][hapmap]
rs6799882	0.88[CHB][hapmap]
rs6799992	0.88[CHB][hapmap]
rs6802787	0.88[CHB][hapmap]
rs6807804	0.88[CHB][hapmap]
rs6808426	0.88[CHB][hapmap]
rs7426815	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7429277	0.88[CHB][hapmap]
rs7429392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7431846	0.88[CHB][hapmap]
rs7433589	0.88[CHB][hapmap]
rs7622658	0.88[CHB][hapmap]
rs7631877	0.88[CHB][hapmap]
rs7645690	0.88[CHB][hapmap]
rs7645700	0.88[CHB][hapmap]
rs7647499	0.94[CHB][hapmap]
rs7653196	0.94[CHB][hapmap]
rs9819246	0.86[CHB][hapmap]
rs9843498	0.88[CHB][hapmap]
rs9855549	0.88[CHB][hapmap]
rs9865411	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
rs4075020	TMEM45A	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100227200-100239400	Weak transcription	Ovary	ovary
2	chr3:100227400-100239400	Weak transcription	Aorta	Aorta
3	chr3:100227400-100239400	Weak transcription	Fetal Stomach	stomach
4	chr3:100235200-100242000	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr3:100235800-100244800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:100236400-100242600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:100237000-100240600	Weak transcription	GM12878-XiMat	blood
8	chr3:100237200-100240600	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr3:100237600-100239200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:100237600-100239400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:100237600-100241600	Weak transcription	HepG2	liver
12	chr3:100237600-100244200	Weak transcription	NH-A	brain
13	chr3:100237800-100239400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:100238000-100244400	Weak transcription	Adipose Nuclei	Adipose
15	chr3:100238000-100244400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:100238000-100252600	Weak transcription	Fetal Intestine Small	intestine
17	chr3:100238000-100265400	Weak transcription	HSMMtube	muscle
18	chr3:100238200-100239400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:100238200-100239400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:100238200-100240400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:100238200-100240600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:100238200-100244400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:100238200-100244400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:100238200-100244400	Weak transcription	HSMM	muscle
25	chr3:100238400-100239600	Weak transcription	Liver	Liver
26	chr3:100238400-100240400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:100238400-100244200	Weak transcription	NHDF-Ad	bronchial
28	chr3:100238600-100239600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr3:100238600-100239800	Weak transcription	NHEK	skin
30	chr3:100238800-100239200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:100238800-100239200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:100238800-100239200	Weak transcription	Fetal Lung	lung
33	chr3:100238800-100239200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
34	chr3:100238800-100240400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:100238800-100240400	Weak transcription	K562	blood
36	chr3:100238800-100243800	Weak transcription	HMEC	breast
37	chr3:100239000-100239200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:100239000-100239800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:100239000-100241000	Strong transcription	Fetal Muscle Leg	muscle
40	chr3:100239000-100244200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:100239000-100244600	Weak transcription	Spleen	Spleen

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