Variant report

Variant	rs3756416
Chromosome Location	chr5:43383502-43383503
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43381240..43383719-chr5:43393017..43394767,2	K562	blood:
2	chr5:43311527..43313591-chr5:43382158..43385097,2	MCF-7	breast:
3	chr5:43065772..43068006-chr5:43383021..43385941,2	MCF-7	breast:
4	chr5:43382764..43385350-chr5:43482506..43485216,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000112972	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10512825	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs10512827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MKK][hapmap];0.95[ASN][1000 genomes]
rs10512828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10805672	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs10805673	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10805674	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10805675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10941620	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs10941621	0.82[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs10941622	0.86[ASN][1000 genomes]
rs10941623	0.86[ASN][1000 genomes]
rs10941628	0.86[ASN][1000 genomes]
rs10941630	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs10941631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10941632	0.95[ASN][1000 genomes]
rs11738086	0.87[ASN][1000 genomes]
rs11739009	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11739665	0.86[ASN][1000 genomes]
rs11740128	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs11741246	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11741797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742171	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs11742712	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11743633	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11747105	0.83[ASN][1000 genomes]
rs11747834	0.86[ASN][1000 genomes]
rs11950040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11950448	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11951515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951584	0.87[ASN][1000 genomes]
rs11956635	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11956936	0.95[ASN][1000 genomes]
rs11956988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11960415	0.95[ASN][1000 genomes]
rs12109933	0.95[ASN][1000 genomes]
rs12189016	0.86[ASN][1000 genomes]
rs12189447	0.86[ASN][1000 genomes]
rs12513864	0.95[ASN][1000 genomes]
rs12514393	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs12514399	0.80[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs12515072	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs12516435	0.89[ASN][1000 genomes]
rs12517362	0.93[ASN][1000 genomes]
rs12518032	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs12518127	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MKK][hapmap];0.95[ASN][1000 genomes]
rs12519554	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs12520012	0.86[ASN][1000 genomes]
rs12520895	0.95[ASN][1000 genomes]
rs12522178	0.86[ASN][1000 genomes]
rs13659	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1389868	0.85[JPT][hapmap]
rs1545753	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1548097	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1564196	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1564197	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs17244818	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2126948	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs2126949	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2169781	0.86[ASN][1000 genomes]
rs2330242	0.95[ASN][1000 genomes]
rs35239179	0.86[ASN][1000 genomes]
rs3733769	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4050485	0.86[ASN][1000 genomes]
rs4288122	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4320264	0.86[ASN][1000 genomes]
rs4373285	0.86[ASN][1000 genomes]
rs4395639	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs4443425	0.82[ASN][1000 genomes]
rs4443426	0.80[CHB][hapmap]
rs4574553	0.86[ASN][1000 genomes]
rs4591755	0.86[ASN][1000 genomes]
rs4866737	0.86[ASN][1000 genomes]
rs4866738	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4866813	0.86[ASN][1000 genomes]
rs4866818	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4866820	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4866821	0.89[ASN][1000 genomes]
rs4866822	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs4866824	0.89[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs4866825	0.92[ASN][1000 genomes]
rs55634155	0.83[ASN][1000 genomes]
rs55759097	0.95[ASN][1000 genomes]
rs55759722	0.89[ASN][1000 genomes]
rs55794239	0.86[ASN][1000 genomes]
rs55992392	0.81[ASN][1000 genomes]
rs56071328	0.86[ASN][1000 genomes]
rs56114604	0.86[ASN][1000 genomes]
rs56185290	0.89[ASN][1000 genomes]
rs56206275	0.81[ASN][1000 genomes]
rs57066570	0.88[ASN][1000 genomes]
rs57401732	0.86[ASN][1000 genomes]
rs58358642	0.89[ASN][1000 genomes]
rs58679159	0.86[ASN][1000 genomes]
rs58966636	0.84[ASN][1000 genomes]
rs59078439	0.86[ASN][1000 genomes]
rs59625262	0.84[ASN][1000 genomes]
rs59814709	0.92[ASN][1000 genomes]
rs60445501	0.86[ASN][1000 genomes]
rs60826019	0.82[ASN][1000 genomes]
rs61627503	0.95[ASN][1000 genomes]
rs66691321	0.86[ASN][1000 genomes]
rs66914803	0.82[ASN][1000 genomes]
rs67497876	0.86[ASN][1000 genomes]
rs67620667	0.95[ASN][1000 genomes]
rs67651757	0.86[ASN][1000 genomes]
rs67817333	0.86[ASN][1000 genomes]
rs6814	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs6860073	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6863246	0.87[ASN][1000 genomes]
rs6867954	0.95[ASN][1000 genomes]
rs6883936	0.91[EUR][1000 genomes]
rs6886499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6887351	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7380703	0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs754527	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs7701642	0.92[CEU][hapmap];0.83[MEX][hapmap];0.87[EUR][1000 genomes]
rs7706402	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7708779	0.81[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs7714027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7720165	0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs7720681	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.94[ASN][1000 genomes]
rs7727047	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7734293	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs922439	0.90[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs9763006	0.85[EUR][1000 genomes]
rs9790987	0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs9942413	0.84[AMR][1000 genomes];0.92[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3756416	NNT	cis	lymphoblastoid	seeQTL
rs3756416	NNT	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43367200-43386400	Weak transcription	Pancreas	Pancrea
2	chr5:43368600-43389800	Weak transcription	Stomach Mucosa	stomach
3	chr5:43368800-43396400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:43369000-43387000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:43369200-43386800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:43370000-43396200	Weak transcription	Primary B cells from cord blood	blood
7	chr5:43371800-43396800	Weak transcription	Small Intestine	intestine
8	chr5:43372200-43396800	Weak transcription	Gastric	stomach
9	chr5:43373200-43396400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:43374600-43396400	Weak transcription	Adipose Nuclei	Adipose
11	chr5:43375000-43387000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:43375000-43396800	Weak transcription	Spleen	Spleen
13	chr5:43375400-43387200	Weak transcription	Thymus	Thymus
14	chr5:43376200-43389800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:43376600-43384800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:43376600-43384800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr5:43376800-43386800	Weak transcription	HMEC	breast
18	chr5:43377000-43387000	Weak transcription	Lung	lung
19	chr5:43377200-43396800	Weak transcription	Colonic Mucosa	Colon
20	chr5:43378600-43396200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:43378800-43396400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:43379000-43384200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr5:43379000-43396400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:43379200-43395800	Weak transcription	Placenta	Placenta
25	chr5:43379400-43388600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:43379600-43384000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr5:43379600-43384400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:43379600-43384400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:43380400-43396400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:43380600-43387000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:43381800-43384400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr5:43381800-43387000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:43382200-43386200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:43382200-43386400	Weak transcription	Primary T cells from cord blood	blood
35	chr5:43382200-43387000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:43382200-43396400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:43382400-43384800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr5:43382600-43383600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr5:43382600-43387200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr5:43382800-43385400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:43382800-43386200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:43382800-43386600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:43383000-43386000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:43383000-43386400	Weak transcription	GM12878-XiMat	blood
45	chr5:43383400-43383800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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