Variant report

Variant	rs28793701
Chromosome Location	chr3:48762683-48762684
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10865952	0.95[ASN][1000 genomes]
rs11557629	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706203	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708022	0.84[AMR][1000 genomes]
rs11708786	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709092	0.80[AMR][1000 genomes]
rs11709246	0.84[AMR][1000 genomes]
rs11713694	0.84[AMR][1000 genomes]
rs11715177	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715835	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719291	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493578	0.95[ASN][1000 genomes]
rs12497850	0.95[ASN][1000 genomes]
rs12715429	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13063223	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070798	0.87[AMR][1000 genomes];0.81[EUR][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	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094900	0.80[AMR][1000 genomes]
rs13316551	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324119	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13324950	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	0.95[ASN][1000 genomes]
rs17080319	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286651	0.80[AMR][1000 genomes]
rs2286652	0.80[AMR][1000 genomes]
rs2302295	0.87[AMR][1000 genomes]
rs28452701	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28567949	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657585	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096717	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34153629	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34477108	0.84[AMR][1000 genomes]
rs34509487	0.84[AMR][1000 genomes]
rs34577723	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.80[AMR][1000 genomes]
rs3821875	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4077495	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858798	0.95[ASN][1000 genomes]
rs4858828	0.95[ASN][1000 genomes]
rs4858831	0.95[ASN][1000 genomes]
rs56735597	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61137521	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67060340	0.80[AMR][1000 genomes]
rs67332931	0.84[AMR][1000 genomes]
rs6788650	0.95[ASN][1000 genomes]
rs71324924	0.84[AMR][1000 genomes]
rs7633840	0.86[ASN][1000 genomes]
rs9811027	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848203	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854034	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877542	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877685	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882549	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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
rs28793701	WDR6	cis	lung	GTEx
rs28793701	WDR6	cis	Adipose Subcutaneous	GTEx
rs28793701	WDR6	cis	Esophagus Mucosa	GTEx
rs28793701	WDR6	cis	Whole Blood	GTEx
rs28793701	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs28793701	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48760600-48765000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:48761600-48764000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:48761600-48764200	Weak transcription	Colonic Mucosa	Colon
4	chr3:48762000-48763800	Weak transcription	Stomach Mucosa	stomach
5	chr3:48762200-48763600	Weak transcription	Rectal Mucosa Donor 31	rectum

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