Variant report

Variant	rs4938011
Chromosome Location	chr11:113247232-113247233
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1003641	0.80[CHD][hapmap]
rs10502173	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1055075	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs1055076	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10891541	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10891542	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10891545	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.90[TSI][hapmap];0.93[ASN][1000 genomes]
rs11214592	0.83[ASN][1000 genomes]
rs1124492	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1124493	0.82[CHD][hapmap]
rs12224538	0.86[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs12225351	0.91[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	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12292113	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12293753	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1943622	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs2155464	0.80[ASN][1000 genomes]
rs2187346	0.91[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs2276070	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2282511	0.80[ASN][1000 genomes]
rs2288159	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs2298489	0.83[CHB][hapmap]
rs2587550	0.80[CHD][hapmap]
rs28712705	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781884	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4590907	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs4938007	0.90[EUR][1000 genomes]
rs4938010	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4938014	0.86[CHB][hapmap];0.86[CHD][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	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6275	0.80[CHD][hapmap]
rs6589372	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6589373	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7109196	0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs7130431	0.86[CHB][hapmap]
rs713233	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs719803	0.91[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7928201	0.91[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7928978	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs7931066	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7949242	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs877138	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs948176	0.91[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4938011	TTC12	cis	Liver	GTEx
rs4938011	TIMM8B	cis	cerebellum	SCAN
rs4938011	TTC12	cis	multi-tissue	Pritchard
rs4938011	TTC12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113203200-113248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:113232200-113257400	Weak transcription	Small Intestine	intestine
3	chr11:113236400-113248200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:113236800-113248400	Weak transcription	Placenta	Placenta
5	chr11:113238000-113248200	Weak transcription	Thymus	Thymus
6	chr11:113239400-113248000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:113239400-113248200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:113239400-113248800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:113239400-113251600	Weak transcription	Aorta	Aorta
10	chr11:113239600-113248200	Weak transcription	Fetal Muscle Leg	muscle
11	chr11:113240000-113248400	Weak transcription	Pancreas	Pancrea
12	chr11:113240200-113248200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr11:113240200-113258400	Weak transcription	Spleen	Spleen
14	chr11:113240800-113255800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr11:113241600-113247600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:113241800-113248200	Weak transcription	Fetal Stomach	stomach
17	chr11:113241800-113257800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:113242000-113253000	Weak transcription	Brain Substantia Nigra	brain
19	chr11:113243200-113247600	Weak transcription	Fetal Thymus	thymus
20	chr11:113244200-113255800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:113244400-113248200	Weak transcription	HSMMtube	muscle
22	chr11:113244400-113256400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr11:113244600-113247400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr11:113244600-113248200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:113244600-113248200	Weak transcription	NHDF-Ad	bronchial
26	chr11:113244600-113248400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:113244600-113254600	Weak transcription	HSMM	muscle
28	chr11:113244800-113247800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:113244800-113247800	Weak transcription	NHEK	skin
30	chr11:113244800-113248000	Weak transcription	NH-A	brain
31	chr11:113244800-113257400	Weak transcription	Lung	lung
32	chr11:113245000-113247400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:113245000-113247800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:113245000-113247800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:113245200-113247600	Weak transcription	HMEC	breast
36	chr11:113245600-113254200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr11:113246200-113248000	Enhancers	Primary B cells from peripheral blood	blood
38	chr11:113246400-113249400	Enhancers	Fetal Heart	heart
39	chr11:113247000-113247400	Weak transcription	Fetal Brain Male	brain
40	chr11:113247000-113248400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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