Variant report

Variant	rs978588
Chromosome Location	chr10:52234904-52234905
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1011881	0.88[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10740714	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10763366	0.82[CHB][hapmap]
rs10763529	0.88[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs10826100	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10826118	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10826126	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11005937	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203377	0.85[ASN][1000 genomes]
rs1203413	0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1203415	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12356922	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1548256	0.89[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs1569962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1569963	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1810576	0.95[EUR][1000 genomes]
rs1916566	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2092996	0.88[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs2099527	0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2117958	0.84[ASN][1000 genomes]
rs2144862	0.88[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs2339505	0.92[CEU][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2339506	0.91[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2574959	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2688878	0.83[ASN][1000 genomes]
rs2842103	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2842111	0.84[ASN][1000 genomes]
rs4312019	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4536155	0.87[ASN][1000 genomes]
rs4935712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4935727	0.89[CEU][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs4935730	0.87[EUR][1000 genomes]
rs7071603	0.89[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs7075289	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7092014	0.84[ASN][1000 genomes]
rs715675	0.83[ASN][1000 genomes]
rs7904833	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52208000-52240200	Weak transcription	Esophagus	oesophagus
2	chr10:52218000-52240200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52220000-52243600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr10:52220400-52237800	Weak transcription	Ovary	ovary
5	chr10:52229800-52242600	Weak transcription	Thymus	Thymus
6	chr10:52229800-52244000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr10:52229800-52252000	Weak transcription	Aorta	Aorta
8	chr10:52230000-52237600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr10:52230000-52240000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr10:52230400-52236200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:52230400-52236400	Weak transcription	Primary B cells from cord blood	blood
12	chr10:52230400-52236400	Weak transcription	Lung	lung
13	chr10:52230400-52240000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr10:52230600-52236000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr10:52230600-52236400	Weak transcription	Fetal Thymus	thymus
16	chr10:52230600-52256400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr10:52231000-52235400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr10:52231000-52235800	Weak transcription	HSMM	muscle
19	chr10:52231000-52236200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr10:52231000-52236200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr10:52231000-52236400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr10:52231000-52237600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr10:52231000-52239400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr10:52231200-52235000	Weak transcription	Brain Hippocampus Middle	brain
25	chr10:52231200-52236200	Weak transcription	Fetal Lung	lung
26	chr10:52231200-52236400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr10:52231200-52236400	Weak transcription	Liver	Liver
28	chr10:52231200-52236400	Weak transcription	Fetal Intestine Large	intestine
29	chr10:52231200-52236400	Weak transcription	Fetal Intestine Small	intestine
30	chr10:52231200-52236400	Weak transcription	Spleen	Spleen
31	chr10:52231200-52240000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr10:52231200-52240200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr10:52231200-52242000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:52231200-52244600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr10:52231200-52257800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr10:52231400-52235200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr10:52231400-52236400	Weak transcription	Primary T cells from cord blood	blood
38	chr10:52231400-52236600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr10:52231400-52238600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr10:52231600-52236400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr10:52231600-52236400	Weak transcription	Placenta	Placenta
42	chr10:52231800-52243000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr10:52232200-52236200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr10:52232400-52242400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr10:52233800-52238000	Weak transcription	Small Intestine	intestine
46	chr10:52234000-52235400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr10:52234000-52237800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr10:52234000-52240200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr10:52234000-52240200	Weak transcription	Gastric	stomach
50	chr10:52234000-52240200	Weak transcription	Right Ventricle	heart

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