Variant report

Variant	rs12480522
Chromosome Location	chr20:24586383-24586384
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11905582	0.82[YRI][hapmap]
rs11906967	0.82[YRI][hapmap]
rs11907274	0.82[YRI][hapmap]
rs12481129	0.95[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12481146	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1326298	1.00[JPT][hapmap]
rs1326301	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs17250061	1.00[JPT][hapmap]
rs17250068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17823746	0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1883923	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1887057	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024608	0.90[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2026565	1.00[JPT][hapmap]
rs2026566	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179800	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2892216	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4813523	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4813524	0.90[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4815282	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815286	0.95[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4815287	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4815288	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4815289	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4815290	0.95[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4815291	0.95[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55770994	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58949684	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6036849	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6036851	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6036854	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6049791	1.00[JPT][hapmap]
rs6049793	1.00[JPT][hapmap]
rs6049811	0.84[MEX][hapmap]
rs60869925	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6114780	1.00[JPT][hapmap]
rs7268862	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73345329	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73345369	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73345393	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8118304	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.93[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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12480522	ABHD12	cis	parietal	SCAN
rs12480522	CST5	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24581800-24590600	Weak transcription	Brain Anterior Caudate	brain
2	chr20:24583200-24599800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr20:24584400-24591000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:24584400-24612600	Weak transcription	Aorta	Aorta
5	chr20:24585200-24591000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr20:24585800-24587000	Enhancers	Brain Hippocampus Middle	brain
7	chr20:24585800-24590800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr20:24586000-24586400	Enhancers	Brain Substantia Nigra	brain
9	chr20:24586000-24586800	Enhancers	Brain Cingulate Gyrus	brain
10	chr20:24586000-24587000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr20:24586000-24590800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:24586200-24586600	Enhancers	Fetal Brain Male	brain

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