Variant report

Variant	rs11720460
Chromosome Location	chr3:49269270-49269271
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10049462	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10154895	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11552724	0.91[EUR][1000 genomes]
rs11706052	0.81[EUR][1000 genomes]
rs11706189	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11710247	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11713297	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11717524	0.92[ASN][1000 genomes]
rs11718982	0.86[EUR][1000 genomes]
rs11719220	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11920267	0.86[ASN][1000 genomes]
rs12631989	0.92[ASN][1000 genomes]
rs12715434	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13064780	0.86[ASN][1000 genomes]
rs13068038	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13072554	0.80[EUR][1000 genomes]
rs13077498	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13096406	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2117938	0.92[ASN][1000 genomes]
rs2334958	0.97[ASN][1000 genomes]
rs28690891	0.81[AFR][1000 genomes]
rs34326553	0.87[EUR][1000 genomes]
rs34343820	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34566463	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34784192	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35060561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35108630	0.81[EUR][1000 genomes]
rs35185152	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35218722	0.86[ASN][1000 genomes]
rs35673421	0.89[EUR][1000 genomes]
rs4955432	0.92[ASN][1000 genomes]
rs5030795	0.91[EUR][1000 genomes]
rs55921200	0.81[EUR][1000 genomes]
rs56306491	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66991555	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67286839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67831908	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71324939	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73084135	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7652746	0.92[ASN][1000 genomes]
rs9311439	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9814987	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9826525	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828310	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9835439	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9837237	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9837625	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9847839	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9850917	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9855123	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9862483	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9870030	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9880088	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9880309	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9990153	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11720460	WDR6	cis	Esophagus Mucosa	GTEx
rs11720460	WDR6	cis	Artery Tibial	GTEx
rs11720460	WDR6	cis	Adipose Subcutaneous	GTEx
rs11720460	WDR6	cis	Whole Blood	GTEx
rs11720460	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49250200-49274000	Weak transcription	Osteobl	bone
2	chr3:49256600-49275800	Weak transcription	NHLF	lung
3	chr3:49263400-49269400	Weak transcription	Ovary	ovary
4	chr3:49266200-49292600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:49266600-49270200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:49266800-49270000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:49267000-49270000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:49268400-49269800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:49268800-49270600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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