Variant report

Variant	rs11647164
Chromosome Location	chr16:65004496-65004497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1025312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10459793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11640810	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11646481	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12708869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12923000	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12923516	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12927264	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12931546	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1520233	0.87[GIH][hapmap];0.82[MEX][hapmap]
rs1607696	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16968039	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1826821	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1845849	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs185393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1864147	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2280394	1.00[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2331446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860056	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35141	0.95[JPT][hapmap]
rs35143	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs35153	0.88[ASN][1000 genomes]
rs35181	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs35183	0.97[ASN][1000 genomes]
rs35184	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs35186	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs35187	0.97[ASN][1000 genomes]
rs35190	0.97[ASN][1000 genomes]
rs35197	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs3760056	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891307	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4967877	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4967879	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4967881	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7195682	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs973199	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9930786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.93[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	nsv948640	chr16:64859061-65112790	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11647164	CMTM1	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:64980000-65005200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr16:64984800-65004600	Weak transcription	Fetal Brain Female	brain
3	chr16:64984800-65005400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr16:64985000-65005200	Weak transcription	Brain Germinal Matrix	brain
5	chr16:64985000-65005800	Weak transcription	Aorta	Aorta
6	chr16:64985000-65011000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:64985400-65005800	Weak transcription	Spleen	Spleen
8	chr16:64985400-65015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:64991400-65032600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr16:64998000-65024800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr16:64998400-65014800	Weak transcription	HUVEC	blood vessel
12	chr16:64999200-65010200	Strong transcription	HSMM	muscle
13	chr16:64999200-65017800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr16:64999200-65017800	Strong transcription	NH-A	brain
15	chr16:64999600-65005000	Weak transcription	Fetal Kidney	kidney
16	chr16:65000000-65005000	Weak transcription	Placenta	Placenta
17	chr16:65000800-65051000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr16:65001200-65006800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr16:65001200-65007000	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr16:65001200-65012600	Strong transcription	Fetal Lung	lung
21	chr16:65002200-65005400	Enhancers	Fetal Heart	heart
22	chr16:65002400-65015200	Weak transcription	Left Ventricle	heart
23	chr16:65002600-65004800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr16:65002600-65004800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr16:65002600-65005800	Weak transcription	Fetal Stomach	stomach
26	chr16:65002600-65016000	Weak transcription	Brain Angular Gyrus	brain
27	chr16:65003000-65005400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr16:65003000-65006200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr16:65003000-65007400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr16:65003000-65008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr16:65003200-65008400	Strong transcription	NHLF	lung
32	chr16:65003400-65006800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr16:65003400-65034000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr16:65003600-65005800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr16:65003600-65006800	Strong transcription	NHDF-Ad	bronchial
36	chr16:65003800-65006600	Strong transcription	Ovary	ovary
37	chr16:65003800-65016000	Weak transcription	Brain Hippocampus Middle	brain
38	chr16:65004000-65006400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr16:65004000-65006600	Weak transcription	Esophagus	oesophagus
40	chr16:65004000-65006800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr16:65004000-65007000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr16:65004200-65005800	Strong transcription	Brain Cingulate Gyrus	brain
43	chr16:65004200-65006600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr16:65004200-65006600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr16:65004200-65006600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr16:65004200-65006800	Strong transcription	Brain Anterior Caudate	brain
47	chr16:65004200-65006800	Strong transcription	HSMMtube	muscle
48	chr16:65004200-65007000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr16:65004200-65008800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr16:65004200-65009600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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