Variant report

Variant	rs7429392
Chromosome Location	chr3:100238060-100238061
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:100237962-100238098	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:100237863-100238153	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr3:100238026-100238196	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr3:100237869-100238069	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr3:100237864-100238260	MCF10A-Er-Src	breast:	n/a	n/a
6	EGR1	chr3:100237833-100238132	K562	blood:	n/a	chr3:100237996-100238011
7	MYC	chr3:100237846-100238115	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr3:100237887-100238193	K562	blood:	n/a	n/a
9	POLR2A	chr3:100237914-100238278	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr3:100237922-100238185	IMR90	lung:	n/a	n/a
11	RCOR1	chr3:100238024-100238537	K562	blood:	n/a	n/a
12	UBTF	chr3:100237974-100238174	K562	blood:	n/a	n/a
13	JUND	chr3:100237894-100238556	K562	blood:	n/a	n/a

Variant related genes	Relation type
TMEM45A	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10936221	0.93[ASW][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap]
rs11719592	0.89[CHB][hapmap]
rs12634317	0.89[CHB][hapmap]
rs12636452	0.89[CHB][hapmap]
rs12639465	0.94[CHB][hapmap]
rs4075020	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]
rs4928048	0.89[CHB][hapmap]
rs4928110	0.89[CHB][hapmap]
rs4928111	0.89[CHB][hapmap]
rs4928112	0.89[CHB][hapmap]
rs60272820	0.81[ASN][1000 genomes]
rs62276556	0.80[ASN][1000 genomes]
rs62276559	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6441300	0.94[CHB][hapmap]
rs6441308	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]
rs6441316	0.89[CHB][hapmap]
rs6441328	0.89[CHB][hapmap]
rs6441329	0.89[CHB][hapmap]
rs66791174	0.80[ASN][1000 genomes]
rs67600559	0.81[ASN][1000 genomes]
rs6777810	0.93[ASW][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap]
rs6780654	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap]
rs6792014	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap]
rs6798264	0.81[ASN][1000 genomes]
rs6799879	0.89[CHB][hapmap]
rs6799882	0.89[CHB][hapmap]
rs6799992	0.89[CHB][hapmap]
rs6802787	0.89[CHB][hapmap]
rs6807804	0.88[CHB][hapmap]
rs6808426	0.89[CHB][hapmap]
rs7426815	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap]
rs7429277	0.89[CHB][hapmap]
rs7431846	0.89[CHB][hapmap]
rs7433589	0.89[CHB][hapmap]
rs7622658	0.89[CHB][hapmap]
rs7631877	0.89[CHB][hapmap]
rs7645690	0.89[CHB][hapmap]
rs7645700	0.89[CHB][hapmap]
rs7647499	0.94[CHB][hapmap]
rs7653196	0.94[CHB][hapmap]
rs9819246	0.86[CHB][hapmap]
rs9843498	0.89[CHB][hapmap]
rs9855549	0.89[CHB][hapmap]
rs9865411	0.89[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7429392	TMEM45A	cis	Whole Blood	GTEx
rs7429392	TMEM45A	cis	multi-tissue	Pritchard
rs7429392	PPP1CB	trans	cerebellum	SCAN

Chromatin state (count:38 , 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	chr3:100235200-100238400	Enhancers	NHDF-Ad	bronchial
5	chr3:100235200-100242000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr3:100235800-100244800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:100236200-100238600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:100236400-100242600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:100236600-100238200	Weak transcription	Fetal Lung	lung
10	chr3:100236800-100238800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr3:100237000-100240600	Weak transcription	GM12878-XiMat	blood
12	chr3:100237200-100239000	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:100237200-100240600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr3:100237400-100238200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:100237400-100238400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:100237400-100238800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:100237400-100239000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:100237600-100238200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:100237600-100238400	Enhancers	Liver	Liver
20	chr3:100237600-100238600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:100237600-100238600	Enhancers	Osteobl	bone
22	chr3:100237600-100238800	Enhancers	HMEC	breast
23	chr3:100237600-100239200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:100237600-100239400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:100237600-100241600	Weak transcription	HepG2	liver
26	chr3:100237600-100244200	Weak transcription	NH-A	brain
27	chr3:100237800-100238200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:100237800-100238200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:100237800-100238200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:100237800-100238200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:100237800-100238200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:100237800-100238600	Enhancers	NHEK	skin
33	chr3:100237800-100239400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:100238000-100238200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:100238000-100244400	Weak transcription	Adipose Nuclei	Adipose
36	chr3:100238000-100244400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:100238000-100252600	Weak transcription	Fetal Intestine Small	intestine
38	chr3:100238000-100265400	Weak transcription	HSMMtube	muscle

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