Variant report

Variant	rs656888
Chromosome Location	chr3:109624645-109624646
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1164205	1.00[ASN][1000 genomes]
rs1164206	1.00[ASN][1000 genomes]
rs581999	0.97[ASN][1000 genomes]
rs582946	0.97[ASN][1000 genomes]
rs586783	0.92[ASN][1000 genomes]
rs591350	0.94[ASN][1000 genomes]
rs601561	0.94[ASN][1000 genomes]
rs603474	0.87[ASN][1000 genomes]
rs605795	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs607043	0.85[ASN][1000 genomes]
rs607450	0.97[ASN][1000 genomes]
rs619279	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.90[ASN][1000 genomes]
rs620464	0.85[ASN][1000 genomes]
rs638718	0.97[ASN][1000 genomes]
rs649118	0.88[ASN][1000 genomes]
rs652762	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs652972	0.98[ASN][1000 genomes]
rs653349	0.91[ASN][1000 genomes]
rs655376	0.97[ASN][1000 genomes]
rs656615	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs662417	0.94[ASN][1000 genomes]
rs686694	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs687239	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs687619	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs688898	0.85[ASN][1000 genomes]
rs776341	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs776343	0.93[ASN][1000 genomes]
rs776344	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009075	chr3:109462019-109800029	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv591270	chr3:109462400-109793785	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1011265	chr3:109474218-109625143	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv877332	chr3:109575764-110186611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1009550	chr3:109577315-109795453	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1839660	chr3:109591203-109678542	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv829666	chr3:109593745-109768652	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2754434	chr3:109604310-109777310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs656888	KIAA1524	cis	parietal	SCAN
rs656888	ATP6V1A	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109624000-109625000	ZNF genes & repeats	Dnd41	blood
2	chr3:109624400-109625000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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