Variant report

Variant	rs55997317
Chromosome Location	chr3:52350745-52350746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10460962	0.96[AFR][1000 genomes]
rs10461028	0.91[AFR][1000 genomes]
rs1077142	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11705963	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706001	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11706108	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11707864	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11707931	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11709658	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11710014	0.89[AFR][1000 genomes]
rs11711934	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714402	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11716017	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11718125	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs123602	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13059674	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075370	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13076890	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13091545	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052053	0.95[AFR][1000 genomes]
rs17052054	0.95[AFR][1000 genomes]
rs17052058	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17052061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052068	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2016575	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2159607	0.82[EUR][1000 genomes]
rs2335640	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28481563	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34238085	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34261027	0.82[EUR][1000 genomes]
rs34355561	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34523877	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762015	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34908451	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35133416	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs352143	0.82[AMR][1000 genomes]
rs35860312	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3752819	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3796343	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs390802	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs498946	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55965068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56352611	0.95[AFR][1000 genomes]
rs56357549	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57441156	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59612757	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61150019	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs634382	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6445385	0.88[AFR][1000 genomes]
rs6445386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66462821	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67248391	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6763882	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67834575	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6794675	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6796333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800707	0.84[EUR][1000 genomes]
rs73088800	0.95[AFR][1000 genomes]
rs7615405	0.89[AFR][1000 genomes]
rs7643570	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs82825	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs887515	0.80[EUR][1000 genomes]
rs9844183	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9861879	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	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

No data

Chromatin state (count:97 , 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	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:52333000-52351600	Weak transcription	Thymus	Thymus
8	chr3:52334000-52351400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:52335400-52351400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:52338400-52351400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:52339800-52351200	Weak transcription	Right Ventricle	heart
12	chr3:52342600-52351200	Weak transcription	Fetal Lung	lung
13	chr3:52342600-52351200	Weak transcription	Pancreas	Pancrea
14	chr3:52343000-52351200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:52343200-52351200	Weak transcription	Gastric	stomach
16	chr3:52343800-52350800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:52344400-52351200	Weak transcription	Ovary	ovary
18	chr3:52344600-52351200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:52344800-52351200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:52344800-52351400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:52345200-52351200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:52345200-52351200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:52345400-52351200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:52345400-52351200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:52345600-52351200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:52345800-52351200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:52345800-52351200	Weak transcription	Fetal Intestine Large	intestine
29	chr3:52345800-52351600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:52345800-52351600	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:52346200-52351200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:52346400-52351400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:52346400-52351400	Weak transcription	Primary T cells from cord blood	blood
34	chr3:52347600-52351200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:52347800-52351200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:52347800-52351200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:52348000-52351200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:52348000-52351200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:52348000-52351600	Weak transcription	NHLF	lung
40	chr3:52348000-52353600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:52348200-52351000	Strong transcription	Fetal Intestine Small	intestine
42	chr3:52348200-52351200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:52348200-52351200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:52348200-52351200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:52348200-52351200	Weak transcription	HMEC	breast
46	chr3:52348200-52351400	Weak transcription	K562	blood
47	chr3:52348200-52351400	Weak transcription	NH-A	brain
48	chr3:52348400-52351200	Weak transcription	Colonic Mucosa	Colon
49	chr3:52348400-52351200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:52348400-52351400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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