Variant report

Variant	rs731370
Chromosome Location	chr9:18887753-18887754
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10124966	0.87[EUR][1000 genomes]
rs10756996	0.80[CEU][hapmap]
rs10963819	0.84[ASN][1000 genomes]
rs1359843	0.89[CEU][hapmap]
rs1368772	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1433826	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1433829	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1433831	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs2104596	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3780222	0.81[CEU][hapmap]
rs3866508	0.83[EUR][1000 genomes]
rs4977454	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4977460	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4977461	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4977462	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6475265	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7026374	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7031202	0.87[EUR][1000 genomes]
rs7873965	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7874517	0.81[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs934482	1.00[CEU][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892698	chr9:18830444-18905289	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs731370	TGM6	trans	parietal	SCAN
rs731370	RRAGA	cis	lymphoblastoid	seeQTL
rs731370	IFNB1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18869400-18887800	Weak transcription	Aorta	Aorta
2	chr9:18878600-18895600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:18879800-18889800	Weak transcription	HSMMtube	muscle
4	chr9:18883200-18888200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr9:18883400-18887800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:18883400-18887800	Weak transcription	Fetal Stomach	stomach
7	chr9:18883600-18888000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:18883800-18888400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:18884600-18888000	Weak transcription	Fetal Muscle Leg	muscle
10	chr9:18885200-18889600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:18885800-18896400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:18886200-18889600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:18886400-18889800	Weak transcription	NHLF	lung
14	chr9:18886800-18887800	Weak transcription	HSMM	muscle
15	chr9:18887000-18890000	Strong transcription	NH-A	brain
16	chr9:18887200-18891000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:18887600-18888000	Strong transcription	NHDF-Ad	bronchial
18	chr9:18887600-18888800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:18887600-18888800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:18887600-18888800	Genic enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links