Variant report

Variant	rs12576690
Chromosome Location	chr11:47321509-47321510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10838694	0.90[AMR][1000 genomes]
rs11039157	0.83[AMR][1000 genomes]
rs11530168	0.93[AMR][1000 genomes]
rs11570058	0.91[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs11570067	0.91[CEU][hapmap];1.00[CHD][hapmap]
rs12221497	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs12573962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12575157	0.81[CEU][hapmap];1.00[MEX][hapmap]
rs12575296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576751	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576935	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12578030	0.81[ASN][1000 genomes]
rs17197619	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17197710	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs17726390	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs17726706	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs17790336	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17790342	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17790390	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17790420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2290149	1.00[MEX][hapmap];0.83[TSI][hapmap]
rs3729989	0.91[CEU][hapmap]
rs3736101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758668	1.00[MEX][hapmap]
rs3758674	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs3816724	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41301449	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41304347	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41310332	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45489595	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4647713	0.81[ASN][1000 genomes]
rs4647720	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4647735	0.87[EUR][1000 genomes]
rs4647736	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4647759	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55764401	0.90[AMR][1000 genomes]
rs56168519	0.93[AMR][1000 genomes]
rs56177220	0.90[AMR][1000 genomes]
rs56825896	0.90[AMR][1000 genomes]
rs61896015	0.83[AMR][1000 genomes]
rs61896047	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61896051	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896054	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897361	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61897855	0.81[ASN][1000 genomes]
rs61897856	0.81[ASN][1000 genomes]
rs61897858	0.81[ASN][1000 genomes]
rs61897859	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7102372	0.81[CEU][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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12576690	ATG13	cis	parietal	SCAN
rs12576690	MDK	cis	parietal	SCAN
rs12576690	MADD	cis	parietal	SCAN
rs12576690	DGKZ	cis	cerebellum	SCAN
rs12576690	PACSIN3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47294600-47355200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr11:47295000-47323600	Strong transcription	Dnd41	blood
3	chr11:47295200-47321600	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr11:47295200-47323800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr11:47295200-47326800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:47295400-47323800	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr11:47295400-47324800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:47295400-47324800	Strong transcription	Fetal Thymus	thymus
9	chr11:47295400-47340200	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr11:47295400-47341000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:47295400-47352600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:47295600-47321800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr11:47295600-47323800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:47295600-47323800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:47295600-47324000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:47295600-47324200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:47295600-47324200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr11:47295600-47338800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:47295800-47322000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:47295800-47322400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:47295800-47340600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:47295800-47352800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr11:47296000-47321800	Strong transcription	Colonic Mucosa	Colon
24	chr11:47296000-47321800	Strong transcription	Ovary	ovary
25	chr11:47296000-47322200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:47296000-47323000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:47296000-47324000	Strong transcription	Primary T cells from cord blood	blood
28	chr11:47296000-47353600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:47296200-47327000	Strong transcription	Adipose Nuclei	Adipose
30	chr11:47296200-47340400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:47296600-47323800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:47298800-47324200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr11:47299400-47324000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:47300000-47341200	Strong transcription	Placenta	Placenta
35	chr11:47303000-47321600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:47303200-47340600	Strong transcription	Hela-S3	cervix
37	chr11:47307400-47322200	Weak transcription	Stomach Mucosa	stomach
38	chr11:47309400-47321600	Strong transcription	NHEK	skin
39	chr11:47309600-47321600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr11:47309600-47321600	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr11:47309800-47321600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:47309800-47321600	Strong transcription	GM12878-XiMat	blood
43	chr11:47310400-47322600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr11:47311200-47326400	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr11:47311800-47348800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr11:47316200-47328200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr11:47316600-47321600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr11:47316800-47324800	Strong transcription	HSMM	muscle
49	chr11:47317000-47321600	Strong transcription	Colon Smooth Muscle	Colon
50	chr11:47317200-47325800	Weak transcription	Pancreas	Pancrea

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