Variant report

Variant	rs686694
Chromosome Location	chr3:109636512-109636513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1164205	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1164206	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2693621	0.84[ASN][1000 genomes]
rs2693634	0.82[ASN][1000 genomes]
rs2700237	0.82[ASN][1000 genomes]
rs2950151	0.82[ASN][1000 genomes]
rs2950152	0.82[ASN][1000 genomes]
rs581999	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs582946	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs586783	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs591010	0.85[ASN][1000 genomes]
rs591350	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs593904	0.82[ASN][1000 genomes]
rs595732	0.82[ASN][1000 genomes]
rs598795	0.82[ASN][1000 genomes]
rs598837	0.82[ASN][1000 genomes]
rs599684	0.82[ASN][1000 genomes]
rs600581	0.82[ASN][1000 genomes]
rs600604	0.82[ASN][1000 genomes]
rs601036	0.82[ASN][1000 genomes]
rs601561	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs604088	0.84[ASN][1000 genomes]
rs605795	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs607043	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs607450	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs610419	0.82[ASN][1000 genomes]
rs614845	0.82[ASN][1000 genomes]
rs617480	0.85[ASN][1000 genomes]
rs619279	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620727	0.85[ASN][1000 genomes]
rs636972	0.82[ASN][1000 genomes]
rs638718	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs642142	0.82[ASN][1000 genomes]
rs649118	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs652762	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.95[ASN][1000 genomes]
rs652972	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs653349	0.81[ASN][1000 genomes]
rs655376	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs656615	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656888	0.90[ASN][1000 genomes]
rs662181	0.82[ASN][1000 genomes]
rs662417	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs666016	0.84[ASN][1000 genomes]
rs667006	0.82[ASN][1000 genomes]
rs671520	0.82[ASN][1000 genomes]
rs686100	0.82[ASN][1000 genomes]
rs687239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687619	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687962	0.82[ASN][1000 genomes]
rs688898	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs689213	0.82[ASN][1000 genomes]
rs776341	0.83[ASN][1000 genomes]
rs776343	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs776344	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	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
7	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs686694	SLC35A5	cis	cerebellum	SCAN
rs686694	ATP6V1A	cis	cerebellum	SCAN
rs686694	KIAA1524	cis	parietal	SCAN
rs686694	C2orf63	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109630000-109642400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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