Variant report

Variant	rs17113959
Chromosome Location	chr10:90649763-90649764
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1029024	0.82[CHB][hapmap]
rs10509555	1.00[EUR][1000 genomes]
rs10509556	0.83[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10509558	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509559	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509560	0.91[CHB][hapmap]
rs11202885	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202906	0.91[CHB][hapmap]
rs11202907	0.91[CHB][hapmap]
rs12242274	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243282	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243621	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12245525	1.00[EUR][1000 genomes]
rs12245668	1.00[EUR][1000 genomes]
rs12247227	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs12254451	1.00[EUR][1000 genomes]
rs12257540	1.00[EUR][1000 genomes]
rs12260572	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261664	0.86[ASN][1000 genomes]
rs12262461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12263461	1.00[EUR][1000 genomes]
rs12264840	0.91[CHB][hapmap]
rs12413277	1.00[EUR][1000 genomes]
rs12414800	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113311	1.00[EUR][1000 genomes]
rs17113344	1.00[EUR][1000 genomes]
rs17113363	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113426	1.00[EUR][1000 genomes]
rs17113457	0.83[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17113476	0.83[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17113724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114000	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114016	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114020	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114057	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114116	0.91[CHB][hapmap]
rs17114143	0.91[CHB][hapmap]
rs17114186	0.91[CHB][hapmap]
rs17114283	0.91[CHB][hapmap]
rs2119685	0.91[CHB][hapmap]
rs2231780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231786	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282122	1.00[EUR][1000 genomes]
rs35996190	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3781206	0.91[CHB][hapmap]
rs3781208	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3814691	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs3816245	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3898173	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898174	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56998609	1.00[EUR][1000 genomes]
rs58673564	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58986570	1.00[EUR][1000 genomes]
rs59661152	1.00[EUR][1000 genomes]
rs60349051	1.00[EUR][1000 genomes]
rs60523093	1.00[EUR][1000 genomes]
rs7070713	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7077019	1.00[EUR][1000 genomes]
rs7078383	0.91[CHB][hapmap]
rs7085698	0.91[CHB][hapmap]
rs7090604	1.00[EUR][1000 genomes]
rs7090631	0.91[CHB][hapmap]
rs7098235	0.91[CHB][hapmap]
rs7098246	1.00[EUR][1000 genomes]
rs73364839	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73364841	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73364851	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74150103	0.86[ASN][1000 genomes]
rs7897521	0.91[CHB][hapmap]
rs7908852	0.91[CHB][hapmap]
rs7913997	1.00[EUR][1000 genomes]
rs7915393	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS 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 target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90641000-90653600	Weak transcription	Gastric	stomach
2	chr10:90641400-90658600	Weak transcription	Brain Angular Gyrus	brain
3	chr10:90641600-90653200	Weak transcription	Colonic Mucosa	Colon
4	chr10:90641800-90653800	Weak transcription	Stomach Mucosa	stomach
5	chr10:90641800-90656400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:90641800-90661800	Weak transcription	Thymus	Thymus
7	chr10:90642000-90650400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr10:90642000-90651000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr10:90642200-90649800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr10:90642200-90656600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr10:90642400-90651200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr10:90642400-90652000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:90642600-90653800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr10:90642800-90656400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:90643200-90651800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr10:90643400-90650400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr10:90643400-90651800	Weak transcription	NH-A	brain
20	chr10:90643600-90650800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr10:90643800-90650000	Enhancers	A549	lung
22	chr10:90643800-90650200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr10:90644200-90652000	Weak transcription	HMEC	breast
24	chr10:90644200-90653400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr10:90644400-90652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:90644600-90652000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr10:90646800-90650400	Weak transcription	HSMM	muscle
28	chr10:90646800-90651800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr10:90646800-90651800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr10:90646800-90651800	Weak transcription	HSMMtube	muscle
31	chr10:90646800-90651800	Weak transcription	NHEK	skin
32	chr10:90646800-90653600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr10:90646800-90656200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:90646800-90656800	Weak transcription	Psoas Muscle	Psoas
35	chr10:90647000-90649800	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr10:90647000-90652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr10:90647200-90649800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr10:90647200-90651800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr10:90647400-90650200	Enhancers	NHLF	lung
40	chr10:90647400-90651800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr10:90647400-90652000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr10:90647400-90656000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr10:90647400-90675200	Weak transcription	Spleen	Spleen
44	chr10:90647400-90681000	Weak transcription	Aorta	Aorta
45	chr10:90647800-90653600	Enhancers	Osteobl	bone
46	chr10:90648000-90652200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr10:90648000-90654200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr10:90648000-90656000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:90648200-90650200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr10:90648200-90652200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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