Variant report

Variant	rs4402582
Chromosome Location	chr16:80063069-80063070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:80061252..80063823-chr16:80117741..80119543,2	MCF-7	breast:
2	chr16:80040089..80044174-chr16:80060281..80063913,4	MCF-7	breast:
3	chr16:80052898..80058811-chr16:80059069..80065197,11	MCF-7	breast:
4	chr16:80040033..80042042-chr16:80061174..80063546,2	K562	blood:
5	chr16:80061244..80063092-chr16:80096922..80099593,2	MCF-7	breast:
6	chr16:80061826..80063381-chr16:80077866..80079603,2	MCF-7	breast:
7	chr16:80012173..80015037-chr16:80061330..80063455,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1115722	0.85[EUR][1000 genomes]
rs11645922	0.98[EUR][1000 genomes]
rs12716881	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12921255	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13333795	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1478505	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1478506	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2199645	0.85[EUR][1000 genomes]
rs34941385	0.84[EUR][1000 genomes]
rs4354957	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs4363873	0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs4365299	0.95[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4407073	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4500741	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4500745	0.87[EUR][1000 genomes]
rs4545830	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4888067	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4889067	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889068	0.95[CEU][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs4889084	0.90[EUR][1000 genomes]
rs4889086	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs4889090	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs4889092	0.90[EUR][1000 genomes]
rs4889093	0.85[EUR][1000 genomes]
rs6564727	0.91[EUR][1000 genomes]
rs6564728	0.86[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs6564729	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6564730	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7184607	0.87[EUR][1000 genomes]
rs7185080	0.85[EUR][1000 genomes]
rs7192544	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs7192753	0.86[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs7193465	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8050142	0.91[CEU][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8050160	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8050173	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8057937	0.84[EUR][1000 genomes]
rs8059251	0.90[EUR][1000 genomes]
rs9937844	0.83[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9940390	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv573294	chr16:80005642-80131944	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4402582	MATR3	trans	cerebellum	SCAN
rs4402582	RFWD3	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80060400-80063600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr16:80060400-80064600	Enhancers	HMEC	breast
3	chr16:80060800-80063400	Enhancers	Fetal Stomach	stomach
4	chr16:80061400-80068800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr16:80061600-80063200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr16:80061600-80064000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr16:80061600-80064000	Enhancers	K562	blood
8	chr16:80061600-80064600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr16:80061600-80065200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:80061800-80063200	Weak transcription	Fetal Intestine Large	intestine
11	chr16:80061800-80063400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr16:80061800-80063400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr16:80062000-80063800	Weak transcription	Fetal Thymus	thymus
14	chr16:80062000-80064600	Enhancers	NHEK	skin
15	chr16:80062000-80068000	Weak transcription	HSMM	muscle
16	chr16:80062000-80069800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr16:80062000-80075000	Weak transcription	NH-A	brain
18	chr16:80062400-80063600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:80062600-80063200	Enhancers	Fetal Intestine Small	intestine
20	chr16:80062800-80064000	Enhancers	Esophagus	oesophagus
21	chr16:80062800-80070200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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