Variant report

Variant	rs12105231
Chromosome Location	chr2:31368997-31368998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10190164	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10201005	0.93[JPT][hapmap]
rs11675787	0.80[ASN][1000 genomes]
rs12989636	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs13408448	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1562023	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17010764	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2008535	0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs57938947	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6543605	0.87[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6543606	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543607	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543609	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6706156	0.84[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6708641	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743542	0.89[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap]
rs6747497	0.80[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs7560152	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7560583	0.82[ASN][1000 genomes]
rs7564367	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7596724	0.84[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs956747	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv873771	chr2:31363732-31416582	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv873772	chr2:31363732-31417863	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv873773	chr2:31363732-31426449	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv873774	chr2:31363732-31432367	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873775	chr2:31363732-31439443	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12105231	SRD5A2	cis	cerebellum	SCAN
rs12105231	EIF2B4	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31361800-31369400	Weak transcription	Right Atrium	heart
2	chr2:31365000-31370600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:31368400-31370800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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