Variant report

Variant	rs12600909
Chromosome Location	chr17:59972171-59972172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10512492	0.90[CEU][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes]
rs11079459	0.86[AMR][1000 genomes]
rs12450560	0.90[CEU][hapmap]
rs12451910	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12452094	0.91[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12452732	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12452742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12600620	0.86[AMR][1000 genomes]
rs12604037	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes]
rs16945692	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16945753	0.91[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs16945756	0.85[AMR][1000 genomes]
rs16945759	0.90[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs16945801	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs2271576	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278812	0.82[JPT][hapmap]
rs3744434	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809753	0.90[CEU][hapmap]
rs3826419	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs4422036	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs4968408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968451	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4968452	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4968454	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968456	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968459	0.82[ASN][1000 genomes]
rs4968460	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4968461	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4968462	0.82[JPT][hapmap]
rs4968463	0.90[AMR][1000 genomes]
rs4968467	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs4968468	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs4988344	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56794817	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58085921	0.83[ASN][1000 genomes]
rs58624595	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59080342	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61169879	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61658218	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7218724	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs7221089	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs73332565	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73332580	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73332598	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73334621	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8065778	0.91[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes]
rs8066964	0.90[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs8074890	0.91[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes]
rs8080599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8081917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9630735	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9630736	0.90[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59941400-59975000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:59941400-60004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:59941400-60004400	Weak transcription	Aorta	Aorta
4	chr17:59941400-60004400	Weak transcription	Pancreas	Pancrea
5	chr17:59941600-59979600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:59941600-59987600	Weak transcription	Right Ventricle	heart
7	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
8	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
9	chr17:59941800-59979200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr17:59941800-59979200	Weak transcription	Brain Angular Gyrus	brain
11	chr17:59942600-60002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:59943600-59989600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:59946600-59989200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr17:59947400-59977400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr17:59948000-59972600	Weak transcription	NHDF-Ad	bronchial
16	chr17:59948000-59981800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr17:59948200-59980600	Weak transcription	HMEC	breast
18	chr17:59948200-59986800	Weak transcription	Fetal Kidney	kidney
19	chr17:59950000-59979200	Weak transcription	NHLF	lung
20	chr17:59950800-59981600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:59951000-59972400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr17:59951400-59992200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:59951600-59989600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr17:59952800-59981400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr17:59953200-59972200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr17:59953800-59985600	Weak transcription	Small Intestine	intestine
27	chr17:59954400-60003800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:59954600-59984800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr17:59955200-59979600	Weak transcription	HSMMtube	muscle
30	chr17:59957600-59973200	Strong transcription	Liver	Liver
31	chr17:59958000-59987600	Weak transcription	Esophagus	oesophagus
32	chr17:59959000-59996800	Weak transcription	Gastric	stomach
33	chr17:59959600-60003600	Weak transcription	Fetal Heart	heart
34	chr17:59959800-59973000	Weak transcription	Primary B cells from cord blood	blood
35	chr17:59962000-59977000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:59962400-59979400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:59963400-59989600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr17:59963600-59974800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:59963600-59975400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr17:59963800-59989600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:59964000-59972200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr17:59964000-59975000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr17:59964000-59983200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr17:59964800-59979200	Weak transcription	Hela-S3	cervix
45	chr17:59965000-59977600	Weak transcription	NHEK	skin
46	chr17:59965200-59976600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr17:59965600-59981400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr17:59966000-59978000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr17:59966000-59984600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr17:59966000-60004200	Weak transcription	Psoas Muscle	Psoas

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