Variant report

Variant	rs12378332
Chromosome Location	chr9:17796377-17796378
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10448159	0.86[CEU][hapmap]
rs10491540	0.95[CEU][hapmap];1.00[CHD][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10810850	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963249	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10963254	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10963258	0.95[CEU][hapmap];1.00[CHD][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10963261	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963262	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963263	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963264	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963265	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10963267	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10963268	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963270	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10963272	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10963273	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10963274	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10963275	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10963276	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10963278	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10963284	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10963288	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10963289	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1114790	0.86[CEU][hapmap];1.00[CHD][hapmap];0.87[TSI][hapmap]
rs12000241	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12005953	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12006023	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12006056	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12377526	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12379450	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12380227	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13284953	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13290434	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13291009	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13291415	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13291891	0.81[EUR][1000 genomes]
rs1536068	0.86[CEU][hapmap]
rs2383041	0.94[CEU][hapmap]
rs34106908	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34701669	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35728688	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36045574	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41305339	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4287033	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4394493	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4416918	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4487880	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4961448	0.85[AMR][1000 genomes]
rs62549703	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7044550	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7865921	0.90[CEU][hapmap]
rs9406734	0.86[CEU][hapmap]
rs9406736	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv613706	chr9:17718918-18090934	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv613707	chr9:17720175-18070475	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv613708	chr9:17720175-18072085	Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1034673	chr9:17739006-17916606	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1023089	chr9:17748811-17919574	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12378332	TTC39B	cis	parietal	SCAN
rs12378332	IFNA13	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17784800-17799400	Weak transcription	Hela-S3	cervix
2	chr9:17787000-17800400	Weak transcription	Fetal Brain Female	brain
3	chr9:17788600-17805400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:17794200-17799400	Weak transcription	Fetal Brain Male	brain
5	chr9:17795000-17797200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:17795400-17796600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:17796000-17812000	Weak transcription	Aorta	Aorta
8	chr9:17796200-17798200	Weak transcription	Brain Germinal Matrix	brain

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