Variant report

Variant	rs6774428
Chromosome Location	chr3:89923845-89923846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11915250	1.00[EUR][1000 genomes]
rs11915838	1.00[EUR][1000 genomes]
rs11923167	0.86[AFR][1000 genomes]
rs11925483	1.00[EUR][1000 genomes]
rs11926348	0.86[AFR][1000 genomes]
rs11926549	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11927661	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11928041	1.00[EUR][1000 genomes]
rs11928160	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11928161	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11928197	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11929614	1.00[EUR][1000 genomes]
rs11929622	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11929639	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1357168	0.82[AFR][1000 genomes]
rs1520591	1.00[EUR][1000 genomes]
rs1915735	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34684257	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55743058	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55744636	1.00[EUR][1000 genomes]
rs55746393	1.00[EUR][1000 genomes]
rs55900084	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55996782	1.00[EUR][1000 genomes]
rs56089352	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56108378	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56158147	1.00[EUR][1000 genomes]
rs56763170	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56956865	1.00[EUR][1000 genomes]
rs56978342	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57057195	1.00[EUR][1000 genomes]
rs57243284	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57601270	1.00[EUR][1000 genomes]
rs57803709	1.00[EUR][1000 genomes]
rs58016519	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58239809	1.00[EUR][1000 genomes]
rs59015121	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59235374	1.00[EUR][1000 genomes]
rs59399871	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59478765	1.00[EUR][1000 genomes]
rs60329202	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60465937	1.00[EUR][1000 genomes]
rs60507817	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60621365	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61257843	1.00[EUR][1000 genomes]
rs61374484	1.00[EUR][1000 genomes]
rs6551442	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6551443	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6774114	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6776405	0.87[AFR][1000 genomes]
rs6777959	1.00[EUR][1000 genomes]
rs6789090	0.89[AFR][1000 genomes]
rs6798157	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6801082	1.00[EUR][1000 genomes]
rs6807535	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6807901	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72912052	1.00[EUR][1000 genomes]
rs72912054	1.00[EUR][1000 genomes]
rs72912058	1.00[EUR][1000 genomes]
rs72912060	1.00[EUR][1000 genomes]
rs72912073	1.00[EUR][1000 genomes]
rs72912077	1.00[EUR][1000 genomes]
rs72912082	1.00[EUR][1000 genomes]
rs72912089	1.00[EUR][1000 genomes]
rs72914023	1.00[EUR][1000 genomes]
rs72914055	1.00[EUR][1000 genomes]
rs72914062	1.00[EUR][1000 genomes]
rs72915828	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72915835	0.87[AFR][1000 genomes]
rs72915840	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72915842	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72915844	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72917631	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72917640	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72917652	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72917689	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72929629	1.00[EUR][1000 genomes]
rs72929635	1.00[EUR][1000 genomes]
rs72929637	1.00[EUR][1000 genomes]
rs72929656	1.00[EUR][1000 genomes]
rs72929658	1.00[EUR][1000 genomes]
rs72929660	1.00[EUR][1000 genomes]
rs73846232	1.00[EUR][1000 genomes]
rs73846237	1.00[EUR][1000 genomes]
rs73846238	1.00[EUR][1000 genomes]
rs73847698	1.00[EUR][1000 genomes]
rs73847700	1.00[EUR][1000 genomes]
rs73847937	1.00[EUR][1000 genomes]
rs7610460	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7628770	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7630224	1.00[EUR][1000 genomes]
rs7653528	0.86[AFR][1000 genomes]
rs939741	1.00[EUR][1000 genomes]
rs9682231	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9682398	1.00[EUR][1000 genomes]
rs9683254	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9714298	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1005444	chr3:89803641-90030755	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1008130	chr3:89837442-90192503	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1010796	chr3:89870548-90192503	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1007181	chr3:89879377-89926155	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1013598	chr3:89879377-90192503	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv536642	chr3:89879377-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1007198	chr3:89897811-90027456	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv999312	chr3:89897811-90030878	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv590966	chr3:89904882-90199759	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89923800-89924200	Active TSS	ES-I3 Cell Line	embryonic stem cell

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