Variant report

Variant	rs662417
Chromosome Location	chr3:109569227-109569228
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1164205	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1164206	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs581999	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582946	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs586783	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591350	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs601561	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603474	0.90[ASN][1000 genomes]
rs605795	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs607043	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs607450	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs619279	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs620464	0.91[ASN][1000 genomes]
rs638718	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs649118	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs652762	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs652972	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs653349	0.84[ASN][1000 genomes]
rs655376	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs656615	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs656888	0.94[ASN][1000 genomes]
rs679711	0.82[ASN][1000 genomes]
rs686694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs687239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs687619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs688898	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs776341	0.81[ASN][1000 genomes]
rs776343	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs776344	0.80[AMR][1000 genomes];0.84[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs662417	ATP6V1A	cis	cerebellum	SCAN
rs662417	KIAA1524	cis	parietal	SCAN
rs662417	SLC35A5	cis	cerebellum	SCAN
rs662417	C2orf63	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109568400-109569600	ZNF genes & repeats	Dnd41	blood

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