Variant report

Variant	rs8046518
Chromosome Location	chr16:80222886-80222887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:80222346..80224215-chr16:80228105..80230290,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11150248	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11150249	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11150250	0.90[AFR][1000 genomes]
rs11640391	0.81[CEU][hapmap];0.81[CHD][hapmap];0.93[MEX][hapmap]
rs11640831	0.93[EUR][1000 genomes]
rs11642380	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11642712	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11646831	0.88[EUR][1000 genomes]
rs11647537	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11648337	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11649346	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11859592	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11866127	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12597962	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12926031	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12926639	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12927541	0.88[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12927726	0.88[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12927869	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12928265	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12928708	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12930060	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13380491	0.88[AMR][1000 genomes]
rs13380610	0.88[AMR][1000 genomes]
rs1478504	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1564222	0.84[AMR][1000 genomes]
rs17727704	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17734652	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17796063	0.85[ASN][1000 genomes]
rs17796688	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1904184	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1904186	0.91[EUR][1000 genomes]
rs2008481	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2061792	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34149818	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34758462	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4300652	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4405565	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57865154	0.87[ASN][1000 genomes]
rs7191912	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7193739	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7201276	0.93[EUR][1000 genomes]
rs8047391	0.81[EUR][1000 genomes]
rs8060188	0.96[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs8060663	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9673176	0.93[EUR][1000 genomes]
rs9935498	0.88[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs9935652	0.93[EUR][1000 genomes]
rs9939067	0.93[EUR][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	nsv833298	chr16:80122337-80314603	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1055228	chr16:80207546-80378842	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1061068	chr16:80207546-80537052	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1064093	chr16:80208443-80333301	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv542985	chr16:80208443-80333301	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1059997	chr16:80209367-80247050	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8046518	VAT1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80210400-80231400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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