Variant report

Variant	rs11716017
Chromosome Location	chr3:52380991-52380992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs1011064	1.00[JPT][hapmap]
rs1077142	0.86[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10865972	1.00[JPT][hapmap]
rs11705963	0.92[EUR][1000 genomes]
rs11706001	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706108	0.92[EUR][1000 genomes]
rs11707864	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707931	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709658	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711934	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11711974	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs11714402	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11718125	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11721277	0.81[AFR][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs123602	0.86[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs123603	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13059674	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13060192	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13071708	1.00[JPT][hapmap]
rs13075370	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076508	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13076890	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13089892	1.00[ASN][1000 genomes]
rs13091360	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13091545	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs13096571	1.00[ASN][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164637	1.00[JPT][hapmap]
rs17052058	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052061	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052068	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016575	0.81[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs2109557	1.00[ASN][1000 genomes]
rs2109558	1.00[JPT][hapmap]
rs2109559	1.00[JPT][hapmap]
rs2159607	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2215466	1.00[JPT][hapmap]
rs2335640	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28481563	0.92[EUR][1000 genomes]
rs2878549	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34181173	1.00[ASN][1000 genomes]
rs34238085	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34261027	0.80[EUR][1000 genomes]
rs34332947	1.00[ASN][1000 genomes]
rs34355561	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523877	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34628357	1.00[ASN][1000 genomes]
rs34762015	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34827613	1.00[ASN][1000 genomes]
rs34908451	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35133416	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	1.00[JPT][hapmap]
rs352144	1.00[JPT][hapmap]
rs352173	1.00[JPT][hapmap]
rs353548	1.00[JPT][hapmap]
rs35860312	0.86[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs35982798	1.00[ASN][1000 genomes]
rs3752819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774409	1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs390802	0.86[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs409803	1.00[JPT][hapmap]
rs419050	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs419604	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs419752	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4312651	1.00[JPT][hapmap]
rs4687614	1.00[JPT][hapmap]
rs4687617	1.00[JPT][hapmap]
rs4687618	1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs498946	0.86[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs55965068	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55997317	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56322342	0.80[AFR][1000 genomes]
rs56357549	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56899118	0.85[AFR][1000 genomes]
rs57441156	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs575476	1.00[ASN][1000 genomes]
rs59612757	0.91[EUR][1000 genomes]
rs61150019	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613519	1.00[JPT][hapmap]
rs61734640	1.00[ASN][1000 genomes]
rs634382	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6445386	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6445486	1.00[JPT][hapmap]
rs6445506	1.00[JPT][hapmap]
rs66462821	0.93[EUR][1000 genomes]
rs67248391	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676034	1.00[JPT][hapmap]
rs6763882	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6794675	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795333	1.00[ASN][1000 genomes]
rs6796333	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6800707	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6810027	1.00[JPT][hapmap]
rs71297391	1.00[ASN][1000 genomes]
rs71297394	1.00[ASN][1000 genomes]
rs71297395	1.00[ASN][1000 genomes]
rs71297396	1.00[ASN][1000 genomes]
rs728408	1.00[JPT][hapmap]
rs73091168	0.85[AFR][1000 genomes]
rs758803	1.00[JPT][hapmap]
rs7620015	1.00[JPT][hapmap]
rs7643570	0.93[EUR][1000 genomes]
rs82825	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes]
rs887514	1.00[JPT][hapmap]
rs887515	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs929528	1.00[JPT][hapmap]
rs9844183	0.86[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[JPT][hapmap]
rs9861879	0.92[EUR][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
2	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
4	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
5	esv3428292	chr3:52376212-52382310	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52352200-52382000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:52352200-52384600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:52354800-52384000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:52364200-52383000	Weak transcription	Fetal Lung	lung
5	chr3:52364800-52394400	Weak transcription	HSMMtube	muscle
6	chr3:52366400-52383000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:52366600-52386600	Weak transcription	Aorta	Aorta
8	chr3:52366800-52383000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:52367600-52384400	Weak transcription	Fetal Kidney	kidney
10	chr3:52368400-52383000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:52373800-52396000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:52374000-52382200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:52374000-52385400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:52374000-52386200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:52374000-52399000	Weak transcription	Stomach Mucosa	stomach
16	chr3:52374000-52407000	Strong transcription	Fetal Intestine Small	intestine
17	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:52375400-52405600	Strong transcription	Lung	lung
19	chr3:52375800-52381000	Strong transcription	Fetal Stomach	stomach
20	chr3:52376400-52402000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:52376800-52384400	Weak transcription	GM12878-XiMat	blood
22	chr3:52377000-52406600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:52377000-52406600	Strong transcription	Liver	Liver
24	chr3:52377200-52390600	Strong transcription	Primary T cells from cord blood	blood
25	chr3:52377200-52405200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:52377400-52382400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:52377400-52384600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr3:52377400-52397400	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr3:52377400-52404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:52377400-52406600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:52377400-52406800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:52377600-52384000	Weak transcription	Fetal Thymus	thymus
33	chr3:52377600-52406200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:52377800-52384400	Strong transcription	Spleen	Spleen
35	chr3:52377800-52406200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:52377800-52407200	Strong transcription	Fetal Intestine Large	intestine
37	chr3:52378200-52391600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:52378400-52381200	Strong transcription	Brain Substantia Nigra	brain
39	chr3:52378400-52400000	Strong transcription	Brain Anterior Caudate	brain
40	chr3:52378400-52401200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:52378400-52401200	Strong transcription	Gastric	stomach
42	chr3:52378400-52401800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:52378600-52384400	Strong transcription	Brain Angular Gyrus	brain
44	chr3:52378600-52389800	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:52378600-52390800	Strong transcription	Thymus	Thymus
46	chr3:52378600-52400000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:52378600-52400200	Strong transcription	Brain Cingulate Gyrus	brain
48	chr3:52378600-52400200	Strong transcription	Brain Hippocampus Middle	brain
49	chr3:52378600-52405000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:52378600-52406800	Strong transcription	Primary neutrophils fromperipheralblood	blood

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