Variant report

Variant	rs2282511
Chromosome Location	chr11:113244177-113244178
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1055075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1055076	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs10891543	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10891546	0.82[CHB][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];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12285457	0.81[ASN][1000 genomes]
rs17115439	0.82[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs1893696	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2155464	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298489	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298490	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2303380	0.81[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3897584	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4601821	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4938009	0.90[YRI][hapmap]
rs4938011	0.80[ASN][1000 genomes]
rs4938012	0.83[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4938013	0.82[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4938015	0.82[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs6589375	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7114433	0.82[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[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs719804	0.90[YRI][hapmap]
rs7945132	0.82[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs877138	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2282511	TTC12	cis	Esophagus Muscularis	GTEx
rs2282511	TTC12	cis	Muscle Skeletal	GTEx
rs2282511	TTC12	cis	Heart Left Ventricle	GTEx
rs2282511	TTC12	cis	lung	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113203200-113248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:113229200-113246800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:113229400-113246600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:113230600-113246400	Weak transcription	Fetal Heart	heart
5	chr11:113231800-113246000	Weak transcription	Fetal Brain Male	brain
6	chr11:113232200-113257400	Weak transcription	Small Intestine	intestine
7	chr11:113236400-113248200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:113236800-113246200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:113236800-113248400	Weak transcription	Placenta	Placenta
10	chr11:113238000-113248200	Weak transcription	Thymus	Thymus
11	chr11:113239400-113244200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr11:113239400-113244200	Weak transcription	Right Ventricle	heart
13	chr11:113239400-113245200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:113239400-113247000	Weak transcription	Left Ventricle	heart
15	chr11:113239400-113248000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr11:113239400-113248200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:113239400-113248800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:113239400-113251600	Weak transcription	Aorta	Aorta
19	chr11:113239600-113246200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr11:113239600-113248200	Weak transcription	Fetal Muscle Leg	muscle
21	chr11:113239800-113247000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:113240000-113245400	Weak transcription	Gastric	stomach
23	chr11:113240000-113248400	Weak transcription	Pancreas	Pancrea
24	chr11:113240200-113245600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr11:113240200-113248200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:113240200-113258400	Weak transcription	Spleen	Spleen
27	chr11:113240600-113245200	Enhancers	HMEC	breast
28	chr11:113240600-113246400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr11:113240800-113244600	Weak transcription	Fetal Intestine Large	intestine
30	chr11:113240800-113244800	Weak transcription	Ovary	ovary
31	chr11:113240800-113255800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:113241000-113246000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:113241000-113246600	Weak transcription	Adipose Nuclei	Adipose
34	chr11:113241600-113244400	Weak transcription	Fetal Intestine Small	intestine
35	chr11:113241600-113247600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr11:113241800-113244200	Weak transcription	Lung	lung
37	chr11:113241800-113244400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr11:113241800-113245200	Weak transcription	Brain Anterior Caudate	brain
39	chr11:113241800-113248200	Weak transcription	Fetal Stomach	stomach
40	chr11:113241800-113257800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:113242000-113253000	Weak transcription	Brain Substantia Nigra	brain
42	chr11:113242400-113245000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:113242800-113244800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:113242800-113245000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:113243000-113244400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:113243000-113244600	Enhancers	HSMM	muscle
47	chr11:113243000-113245000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:113243200-113247600	Weak transcription	Fetal Thymus	thymus
49	chr11:113243400-113245600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr11:113243600-113244400	Enhancers	NHLF	lung

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