Variant report

Variant	rs9297589
Chromosome Location	chr8:119539320-119539321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10090804	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs10097320	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10104444	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10104761	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10110626	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10111755	0.93[JPT][hapmap];0.83[MEX][hapmap]
rs10113428	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[ASN][1000 genomes]
rs11774748	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11774993	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs12541156	0.85[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs12541178	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs12545989	0.83[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs12548521	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs12549010	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs12678125	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs13269467	0.84[ASN][1000 genomes]
rs13278633	0.87[ASN][1000 genomes]
rs13280603	0.85[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs2515027	0.85[ASN][1000 genomes]
rs2515055	0.85[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2515056	0.85[ASN][1000 genomes]
rs2515059	0.85[ASN][1000 genomes]
rs28574967	0.87[ASN][1000 genomes]
rs4327885	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs4495457	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4559272	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4625062	0.85[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs6469752	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6469754	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6982778	0.86[ASN][1000 genomes]
rs6984080	0.90[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7004852	0.96[CEU][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7012653	0.83[ASN][1000 genomes]
rs7823933	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7823939	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7825490	0.83[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs7825771	0.84[ASN][1000 genomes]
rs7826003	0.93[JPT][hapmap]
rs7836391	0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032681	chr8:119153316-119609948	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv539737	chr8:119153316-119609948	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831443	chr8:119390590-119590662	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9297589	MAL2	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119536600-119539400	Weak transcription	Brain Anterior Caudate	brain
2	chr8:119537200-119539800	Enhancers	Brain Hippocampus Middle	brain
3	chr8:119537400-119539800	Enhancers	Brain Cingulate Gyrus	brain
4	chr8:119537600-119539600	Enhancers	Brain Angular Gyrus	brain
5	chr8:119538000-119539400	Enhancers	Brain Substantia Nigra	brain
6	chr8:119538000-119539800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr8:119538400-119539800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr8:119538800-119539400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr8:119538800-119539400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:119538800-119539400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr8:119538800-119539600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr8:119538800-119539600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr8:119539000-119541200	Weak transcription	GM12878-XiMat	blood
14	chr8:119539200-119539400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr8:119539200-119539600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr8:119539200-119539600	Enhancers	NHLF	lung
17	chr8:119539200-119540800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr8:119539200-119542600	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links