Variant report

Variant	rs56735597
Chromosome Location	chr3:48765168-48765169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11557629	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11706203	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11706983	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11708022	0.84[AMR][1000 genomes]
rs11708786	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11709092	0.80[AMR][1000 genomes]
rs11709246	0.84[AMR][1000 genomes]
rs11713694	0.84[AMR][1000 genomes]
rs11715177	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11715689	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11715835	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11719291	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12715429	0.87[AMR][1000 genomes]
rs13063223	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13070798	0.87[AMR][1000 genomes]
rs13073997	0.84[AMR][1000 genomes]
rs13074318	0.84[AMR][1000 genomes]
rs13084000	0.84[AMR][1000 genomes]
rs13087930	0.84[AMR][1000 genomes]
rs13090013	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13094900	0.80[AMR][1000 genomes]
rs13316551	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13324119	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13324950	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13434258	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17080319	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2286651	0.80[AMR][1000 genomes]
rs2286652	0.80[AMR][1000 genomes]
rs2302295	0.87[AMR][1000 genomes]
rs28452701	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28567949	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28657585	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28793701	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34096717	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs34153629	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34477108	0.84[AMR][1000 genomes]
rs34509487	0.84[AMR][1000 genomes]
rs34577723	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35064573	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3733086	0.80[AMR][1000 genomes]
rs3821875	0.80[AMR][1000 genomes]
rs4077495	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61137521	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67060340	0.80[AMR][1000 genomes]
rs67332931	0.84[AMR][1000 genomes]
rs71324924	0.84[AMR][1000 genomes]
rs9811027	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9834996	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9848203	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9854034	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9877542	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9877685	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9882549	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs56735597	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs56735597	WDR6	cis	Esophagus Mucosa	GTEx
rs56735597	WDR6	cis	lung	GTEx
rs56735597	WDR6	cis	Adipose Subcutaneous	GTEx
rs56735597	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs56735597	WDR6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48763800-48766200	Enhancers	Stomach Mucosa	stomach
2	chr3:48764000-48766200	Enhancers	Rectal Mucosa Donor 29	rectum
3	chr3:48764200-48765400	Enhancers	Colonic Mucosa	Colon
4	chr3:48764800-48765200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:48764800-48765200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
6	chr3:48765000-48765200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:48765000-48765200	Bivalent Enhancer	Fetal Stomach	stomach
8	chr3:48765000-48765400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:48765000-48765400	Enhancers	Sigmoid Colon	Sigmoid Colon

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