Variant report

Variant	rs17052058
Chromosome Location	chr3:52344680-52344681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52340180..52343707-chr3:52344223..52347633,5	K562	blood:
2	chr3:52342653..52345126-chr3:52346382..52348341,2	K562	blood:
3	chr3:52334304..52337060-chr3:52343020..52346051,4	K562	blood:
4	chr3:52344151..52347249-chr3:52349398..52352929,3	K562	blood:

Variant related genes	Relation type
ENSG00000114841	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs1011064	1.00[JPT][hapmap]
rs10460962	0.83[ASW][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes]
rs10461028	0.91[AFR][1000 genomes]
rs1077142	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10865972	1.00[JPT][hapmap]
rs11705963	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11706001	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11706108	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11707864	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11707931	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11709658	0.86[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11710014	0.89[LWK][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs11711934	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11711974	0.84[LWK][hapmap]
rs11714402	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11716017	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11718125	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[JPT][hapmap]
rs123602	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs123603	1.00[JPT][hapmap]
rs13059674	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13060192	1.00[JPT][hapmap]
rs13071708	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13075370	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13076508	1.00[JPT][hapmap]
rs13076890	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13091360	1.00[JPT][hapmap]
rs13091545	0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164637	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17052053	0.83[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs17052054	0.83[ASW][hapmap];0.94[LWK][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes]
rs17052061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17052068	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2016575	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2109558	1.00[JPT][hapmap]
rs2109559	1.00[JPT][hapmap]
rs2159607	0.93[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2215466	1.00[JPT][hapmap]
rs2335640	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28481563	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2878549	1.00[JPT][hapmap]
rs34238085	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34261027	0.81[EUR][1000 genomes]
rs34355561	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34523877	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34551211	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34762015	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34908451	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35133416	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs352142	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs352143	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs352144	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs352173	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs353548	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35860312	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3733063	0.86[LWK][hapmap];0.82[YRI][hapmap]
rs3752819	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3774409	1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390802	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4082828	0.81[LWK][hapmap]
rs409803	1.00[JPT][hapmap]
rs419050	1.00[JPT][hapmap]
rs419604	1.00[JPT][hapmap]
rs419752	1.00[JPT][hapmap]
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]
rs498946	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55965068	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55997317	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56352611	0.95[AFR][1000 genomes]
rs56357549	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57441156	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59612757	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61150019	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap]
rs634382	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6445385	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs6445386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6445486	1.00[JPT][hapmap]
rs6445506	1.00[JPT][hapmap]
rs66462821	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67248391	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap]
rs6763882	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6793317	0.83[LWK][hapmap];0.88[MKK][hapmap]
rs6794675	0.89[EUR][1000 genomes]
rs6796333	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6800707	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6809248	0.81[YRI][hapmap]
rs6810027	1.00[JPT][hapmap]
rs728408	1.00[JPT][hapmap]
rs73088800	0.95[AFR][1000 genomes]
rs758803	1.00[JPT][hapmap]
rs7615405	0.89[AFR][1000 genomes]
rs7620015	1.00[JPT][hapmap]
rs7643570	0.91[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs82825	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs887514	1.00[JPT][hapmap]
rs887515	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs929528	1.00[JPT][hapmap]
rs9844183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[JPT][hapmap]
rs9861879	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	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
4	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
5	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17052058	ITIH3	cis	parietal	SCAN
rs17052058	DNAH1	cis	cerebellum	SCAN
rs17052058	GNAT1	cis	parietal	SCAN
rs17052058	SEMA3G	cis	cerebellum	SCAN
rs17052058	DNAH1	cis	parietal	SCAN
rs17052058	ZNF589	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
2	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:52328000-52347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
5	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:52330200-52345400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:52333000-52351600	Weak transcription	Thymus	Thymus
10	chr3:52334000-52351400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:52334200-52347400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:52334200-52349600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:52334400-52347200	Weak transcription	Esophagus	oesophagus
14	chr3:52334600-52348000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:52335000-52347600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:52335200-52345000	Weak transcription	HSMMtube	muscle
17	chr3:52335200-52347200	Weak transcription	Left Ventricle	heart
18	chr3:52335200-52347400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:52335200-52347600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:52335400-52345000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:52335400-52351400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:52337200-52345000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:52337400-52347200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:52338400-52351400	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:52339400-52347400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:52339800-52351200	Weak transcription	Right Ventricle	heart
27	chr3:52341800-52347000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:52342000-52345200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:52342000-52347600	Weak transcription	K562	blood
30	chr3:52342200-52344800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:52342200-52344800	Strong transcription	Adipose Nuclei	Adipose
32	chr3:52342200-52344800	Strong transcription	Liver	Liver
33	chr3:52342200-52347400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:52342400-52345000	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:52342600-52344800	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr3:52342600-52345000	Weak transcription	Fetal Thymus	thymus
37	chr3:52342600-52347200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:52342600-52351200	Weak transcription	Fetal Lung	lung
39	chr3:52342600-52351200	Weak transcription	Pancreas	Pancrea
40	chr3:52342800-52344800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:52342800-52345200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:52342800-52347400	Weak transcription	Small Intestine	intestine
43	chr3:52343000-52344800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:52343000-52345200	Weak transcription	HepG2	liver
45	chr3:52343000-52345400	Strong transcription	Fetal Stomach	stomach
46	chr3:52343000-52347400	Weak transcription	Colonic Mucosa	Colon
47	chr3:52343000-52348000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:52343000-52351200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:52343200-52344800	Strong transcription	Placenta	Placenta
50	chr3:52343200-52345000	Strong transcription	Fetal Intestine Small	intestine

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