Variant report

Variant	rs13333795
Chromosome Location	chr16:80063745-80063746
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	chr16:80063723..80065397-chr16:80069694..80072039,2	MCF-7	breast:

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	0.97[EUR][1000 genomes]
rs12716881	0.95[EUR][1000 genomes]
rs12921255	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1478505	0.90[EUR][1000 genomes]
rs1478506	0.90[EUR][1000 genomes]
rs2199645	0.84[EUR][1000 genomes]
rs34941385	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4354957	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs4363873	0.82[EUR][1000 genomes]
rs4365299	0.95[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4402582	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4407073	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs4500741	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4500745	0.87[EUR][1000 genomes]
rs4545830	0.82[EUR][1000 genomes]
rs4888067	0.93[EUR][1000 genomes]
rs4889067	0.94[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4889068	0.95[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs4889084	0.89[EUR][1000 genomes]
rs4889086	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs4889090	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs4889092	0.89[EUR][1000 genomes]
rs4889093	0.84[EUR][1000 genomes]
rs6564727	0.90[EUR][1000 genomes]
rs6564728	0.86[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs6564729	0.89[EUR][1000 genomes]
rs6564730	0.89[EUR][1000 genomes]
rs7184607	0.86[EUR][1000 genomes]
rs7185080	0.85[EUR][1000 genomes]
rs7192544	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs7192753	0.86[CEU][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs7193465	0.88[ASW][hapmap];0.83[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs8050142	0.91[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs8050160	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs8050173	0.82[EUR][1000 genomes]
rs8057937	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8059251	0.89[EUR][1000 genomes]
rs9937844	0.94[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9940390	0.82[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
rs13333795	MATR3	trans	cerebellum	SCAN
rs13333795	RFWD3	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80060400-80064600	Enhancers	HMEC	breast
2	chr16:80061400-80068800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:80061600-80064000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr16:80061600-80064000	Enhancers	K562	blood
5	chr16:80061600-80064600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr16:80061600-80065200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr16:80062000-80063800	Weak transcription	Fetal Thymus	thymus
8	chr16:80062000-80064600	Enhancers	NHEK	skin
9	chr16:80062000-80068000	Weak transcription	HSMM	muscle
10	chr16:80062000-80069800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr16:80062000-80075000	Weak transcription	NH-A	brain
12	chr16:80062800-80064000	Enhancers	Esophagus	oesophagus
13	chr16:80062800-80070200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr16:80063200-80063800	Weak transcription	Fetal Intestine Small	intestine
15	chr16:80063200-80064200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr16:80063200-80064400	Enhancers	Fetal Intestine Large	intestine
17	chr16:80063400-80067000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr16:80063600-80064400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:80063600-80064800	Enhancers	Ovary	ovary
20	chr16:80063600-80067200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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