Variant report

Variant	rs1055076
Chromosome Location	chr11:113239709-113239710
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANKK1-2	chr11:113239200-113239839	ENSG00000270179.1

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10502173	0.83[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs1055075	0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs10891541	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10891542	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10891545	0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.90[TSI][hapmap];0.92[ASN][1000 genomes]
rs11214592	0.84[ASN][1000 genomes]
rs1124492	0.81[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12224538	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs12225351	0.83[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs12285457	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12292113	0.83[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12293753	0.83[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1943622	0.83[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs2155464	0.81[ASN][1000 genomes]
rs2187346	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs2276070	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282511	0.81[ASN][1000 genomes]
rs2288159	0.83[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2298489	0.83[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs28712705	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3781884	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4590907	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs4938007	0.91[EUR][1000 genomes]
rs4938010	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4938011	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4938014	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs4987094	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs61492892	0.90[ASN][1000 genomes]
rs6589372	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6589373	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7109196	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs7130431	0.86[CHB][hapmap];0.91[CHD][hapmap];0.80[ASN][1000 genomes]
rs713233	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs719803	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7928201	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7928978	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs7931066	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7949242	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs877138	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs948176	0.83[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556444	chr11:113234432-113383394	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1055076	TIMM8B	cis	cerebellum	SCAN
rs1055076	TTC12	Cis_1M	lymphoblastoid	RTeQTL
rs1055076	TTC12	cis	multi-tissue	Pritchard

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113195600-113240600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:113203200-113248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:113204000-113240600	Weak transcription	Stomach Mucosa	stomach
4	chr11:113210600-113243600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr11:113213000-113243000	Weak transcription	NHLF	lung
6	chr11:113215400-113243600	Weak transcription	Osteobl	bone
7	chr11:113226600-113242400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr11:113227400-113239800	Strong transcription	Liver	Liver
9	chr11:113227400-113241200	Weak transcription	Psoas Muscle	Psoas
10	chr11:113227800-113241000	Strong transcription	Adipose Nuclei	Adipose
11	chr11:113228400-113240200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr11:113228400-113240800	Strong transcription	Fetal Intestine Large	intestine
13	chr11:113228600-113241600	Strong transcription	Fetal Intestine Small	intestine
14	chr11:113229200-113240400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:113229200-113246800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:113229400-113246600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:113229800-113243800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:113230200-113239800	Weak transcription	Primary B cells from cord blood	blood
19	chr11:113230400-113241000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:113230400-113243800	Weak transcription	HSMMtube	muscle
21	chr11:113230600-113246400	Weak transcription	Fetal Heart	heart
22	chr11:113231800-113246000	Weak transcription	Fetal Brain Male	brain
23	chr11:113232000-113243800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:113232200-113257400	Weak transcription	Small Intestine	intestine
25	chr11:113233200-113240000	Strong transcription	Brain Anterior Caudate	brain
26	chr11:113233400-113239800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:113233400-113240000	Strong transcription	Brain Substantia Nigra	brain
28	chr11:113233400-113240000	Strong transcription	Gastric	stomach
29	chr11:113233400-113240200	Strong transcription	Spleen	Spleen
30	chr11:113233800-113241400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:113235000-113240000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:113235000-113243600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:113235400-113243000	Weak transcription	HSMM	muscle
34	chr11:113235800-113240000	Strong transcription	HMEC	breast
35	chr11:113236000-113240600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:113236000-113241000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:113236200-113243000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr11:113236400-113240400	Weak transcription	Colonic Mucosa	Colon
39	chr11:113236400-113241200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr11:113236400-113243400	Weak transcription	Fetal Lung	lung
41	chr11:113236400-113248200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:113236600-113241200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr11:113236800-113243600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr11:113236800-113246200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:113236800-113248400	Weak transcription	Placenta	Placenta
46	chr11:113237000-113240200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:113237000-113241000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:113237200-113240200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr11:113237200-113240600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:113237200-113241000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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