Variant report

Variant	rs11960415
Chromosome Location	chr5:43367509-43367510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs10039048	0.83[EUR][1000 genomes]
rs10039617	0.83[EUR][1000 genomes]
rs10512825	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10512827	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512828	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805672	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10805673	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10805674	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10805675	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10941620	0.81[ASN][1000 genomes]
rs10941621	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10941622	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10941623	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10941628	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10941630	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10941631	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10941632	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738086	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11739009	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11739665	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11740128	0.81[ASN][1000 genomes]
rs11741246	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11741797	0.95[ASN][1000 genomes]
rs11742171	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11742712	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11743622	0.88[EUR][1000 genomes]
rs11743633	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11746629	0.81[ASN][1000 genomes]
rs11747105	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11747834	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11950040	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950448	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11951515	0.95[ASN][1000 genomes]
rs11951584	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11956635	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956988	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12109933	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189016	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12189447	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12513864	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514393	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12514399	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12515072	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12516435	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12517362	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12518032	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12518127	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519554	0.81[ASN][1000 genomes]
rs12520012	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12520895	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522178	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13187876	0.91[EUR][1000 genomes]
rs13659	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1545753	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1548097	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1564196	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1564197	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1564198	0.88[EUR][1000 genomes]
rs2126948	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2126949	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2169781	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2330242	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35231094	0.81[ASN][1000 genomes]
rs35239179	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3733768	0.82[EUR][1000 genomes]
rs3733769	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3756416	0.95[ASN][1000 genomes]
rs4050485	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4288122	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4320264	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4373285	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4395639	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4443425	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4574553	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4591755	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4866737	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4866738	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4866741	0.90[EUR][1000 genomes]
rs4866813	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4866820	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4866821	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4866822	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4866824	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4866825	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4866826	0.88[EUR][1000 genomes]
rs55634155	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55647314	0.81[EUR][1000 genomes]
rs55759097	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55759722	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55794239	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55800451	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55992392	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56023994	0.82[EUR][1000 genomes]
rs56029402	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56071328	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56114604	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56185290	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56206275	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57066570	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57392430	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57401732	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58358642	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58679159	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58966636	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59078439	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59625262	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59814709	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60445501	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61627503	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451684	0.83[EUR][1000 genomes]
rs66585077	0.81[ASN][1000 genomes]
rs66691321	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66914803	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67415672	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67497876	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67620667	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67651757	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67817333	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6814	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6860073	0.86[ASN][1000 genomes]
rs6863246	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6863360	0.82[EUR][1000 genomes]
rs6867954	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886499	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887351	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6898398	0.81[EUR][1000 genomes]
rs7380703	0.88[ASN][1000 genomes]
rs7445066	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7701391	0.82[EUR][1000 genomes]
rs7704588	0.87[EUR][1000 genomes]
rs7706402	0.94[ASN][1000 genomes]
rs7708779	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7714027	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714919	0.80[EUR][1000 genomes]
rs7716091	0.88[EUR][1000 genomes]
rs7720165	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7720681	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7722781	0.88[EUR][1000 genomes]
rs7727047	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7734293	0.81[ASN][1000 genomes]
rs922439	0.91[ASN][1000 genomes]
rs9292871	0.82[EUR][1000 genomes]
rs9292874	0.88[EUR][1000 genomes]
rs9790987	0.88[EUR][1000 genomes];0.88[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	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11960415	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43364000-43367800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:43366600-43372400	Enhancers	Fetal Intestine Large	intestine
3	chr5:43366600-43372400	Enhancers	Fetal Intestine Small	intestine
4	chr5:43367000-43368200	Enhancers	HepG2	liver
5	chr5:43367000-43369200	Enhancers	Duodenum Mucosa	Duodenum
6	chr5:43367200-43368200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:43367200-43386400	Weak transcription	Pancreas	Pancrea
8	chr5:43367400-43376600	Weak transcription	Colonic Mucosa	Colon

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