Variant report

Variant	rs1055075
Chromosome Location	chr11:113239512-113239513
allele	C/T
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: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1055076	0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs10891543	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10891546	0.82[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs11214579	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12282356	0.81[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12285457	0.81[ASN][1000 genomes]
rs17115439	0.82[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs1893696	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2155464	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282511	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298489	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298490	0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2303380	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3897584	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4601821	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4938009	0.90[YRI][hapmap]
rs4938011	0.80[ASN][1000 genomes]
rs4938012	0.82[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4938013	0.82[CHB][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4938015	0.82[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs6589375	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7114433	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7115082	0.86[ASN][1000 genomes]
rs7123797	0.82[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7130431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs719802	0.84[CHD][hapmap]
rs719804	0.90[YRI][hapmap]
rs7945132	0.82[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs877138	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1055075	TTC12	cis	Heart Left Ventricle	GTEx
rs1055075	TTC12	cis	cerebellum	SCAN
rs1055075	TTC12	cis	parietal	SCAN
rs1055075	TTC12	cis	Esophagus Muscularis	GTEx
rs1055075	TTC12	cis	Muscle Skeletal	GTEx
rs1055075	TTC12	cis	lung	GTEx

Chromatin state (count:96 , 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	chr11:113228200-113239600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr11:113228400-113239600	Strong transcription	Fetal Muscle Leg	muscle
13	chr11:113228400-113240200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr11:113228400-113240800	Strong transcription	Fetal Intestine Large	intestine
15	chr11:113228600-113241600	Strong transcription	Fetal Intestine Small	intestine
16	chr11:113229200-113240400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:113229200-113246800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:113229400-113246600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr11:113229800-113243800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:113230200-113239800	Weak transcription	Primary B cells from cord blood	blood
21	chr11:113230400-113241000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:113230400-113243800	Weak transcription	HSMMtube	muscle
23	chr11:113230600-113246400	Weak transcription	Fetal Heart	heart
24	chr11:113231800-113246000	Weak transcription	Fetal Brain Male	brain
25	chr11:113232000-113243800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:113232200-113257400	Weak transcription	Small Intestine	intestine
27	chr11:113233200-113240000	Strong transcription	Brain Anterior Caudate	brain
28	chr11:113233400-113239800	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:113233400-113240000	Strong transcription	Brain Substantia Nigra	brain
30	chr11:113233400-113240000	Strong transcription	Gastric	stomach
31	chr11:113233400-113240200	Strong transcription	Spleen	Spleen
32	chr11:113233800-113239600	Strong transcription	Fetal Stomach	stomach
33	chr11:113233800-113241400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr11:113234800-113239600	Strong transcription	NHEK	skin
35	chr11:113235000-113240000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:113235000-113243600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:113235200-113239600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:113235400-113243000	Weak transcription	HSMM	muscle
39	chr11:113235600-113239600	Weak transcription	GM12878-XiMat	blood
40	chr11:113235800-113240000	Strong transcription	HMEC	breast
41	chr11:113236000-113240600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:113236000-113241000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:113236200-113243000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr11:113236400-113240400	Weak transcription	Colonic Mucosa	Colon
45	chr11:113236400-113241200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:113236400-113243400	Weak transcription	Fetal Lung	lung
47	chr11:113236400-113248200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:113236600-113241200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr11:113236800-113243600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:113236800-113246200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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