Variant report

Variant	rs58239809
Chromosome Location	chr3:89749917-89749918
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11915250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11915838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11920932	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11925483	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926549	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11928041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11929607	0.83[AMR][1000 genomes]
rs11929622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11929639	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1520591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2347535	0.83[AMR][1000 genomes]
rs55744636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55746393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55996782	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56062637	1.00[AMR][1000 genomes]
rs56158147	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56956865	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57057195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57803709	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59235374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59478765	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60465937	1.00[EUR][1000 genomes]
rs60507817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60621365	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61257843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61374484	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762985	0.83[AMR][1000 genomes]
rs6774114	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6774428	1.00[EUR][1000 genomes]
rs6774549	0.83[AMR][1000 genomes]
rs6777959	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6798157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72912052	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72912054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72912058	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72912060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72912073	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72912077	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72912082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72912089	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72914023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72914055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72914062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72915828	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72915840	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72915842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72915844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72929629	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72929635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72929637	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72929656	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72929658	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72929660	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73846232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73846237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73846238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73847698	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73847700	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7616622	0.94[AFR][1000 genomes]
rs7628770	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682231	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682398	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9683254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1010932	chr3:89424428-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1010021	chr3:89521983-90141988	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv530024	chr3:89548440-90304841	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv869889	chr3:89653238-90087372	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1013502	chr3:89670525-89915342	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv536641	chr3:89670525-89915342	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv834761	chr3:89718508-89877335	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89746200-89750600	Enhancers	Duodenum Mucosa	Duodenum
2	chr3:89747200-89750200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:89749000-89750400	Enhancers	Colonic Mucosa	Colon
4	chr3:89749800-89750400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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