Variant report

Variant	rs3760056
Chromosome Location	chr16:65040328-65040329
allele	G/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];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10459793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640810	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11646481	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11647164	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]
rs12708869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12923000	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12923516	0.87[EUR][1000 genomes]
rs12927264	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12931546	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1520233	0.87[GIH][hapmap];0.82[MEX][hapmap]
rs1607696	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16968039	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1826821	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1845849	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs185393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1864147	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2280394	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2331446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2860056	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35141	0.95[JPT][hapmap]
rs35143	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs35153	0.86[ASN][1000 genomes]
rs35181	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs35183	0.99[ASN][1000 genomes]
rs35184	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35186	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35187	0.99[ASN][1000 genomes]
rs35190	0.99[ASN][1000 genomes]
rs35197	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs3826240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3891307	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4967877	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4967879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967881	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7195682	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs973199	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9930786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.93[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	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
rs3760056	CMTM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:65000800-65051000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr16:65017200-65041800	Weak transcription	Colon Smooth Muscle	Colon
3	chr16:65022000-65041200	Weak transcription	Fetal Heart	heart
4	chr16:65023400-65043200	Strong transcription	Fetal Lung	lung
5	chr16:65025800-65051400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr16:65032200-65043400	Weak transcription	Fetal Brain Male	brain
7	chr16:65033800-65040400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr16:65035200-65042000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr16:65036000-65051400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr16:65036400-65043400	Weak transcription	Brain Substantia Nigra	brain
11	chr16:65036400-65043600	Weak transcription	Brain Hippocampus Middle	brain
12	chr16:65036600-65041400	Strong transcription	HSMM	muscle
13	chr16:65036600-65043600	Weak transcription	Brain Angular Gyrus	brain
14	chr16:65037000-65043800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr16:65037000-65044000	Strong transcription	Osteobl	bone
16	chr16:65037200-65041000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr16:65037200-65041400	Strong transcription	NHLF	lung
18	chr16:65037200-65041600	Strong transcription	Fetal Stomach	stomach
19	chr16:65037400-65040600	Strong transcription	Fetal Muscle Leg	muscle
20	chr16:65037400-65040600	Strong transcription	NH-A	brain
21	chr16:65037400-65040800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr16:65037600-65041200	Strong transcription	Fetal Kidney	kidney
23	chr16:65037600-65042000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr16:65037800-65040600	Strong transcription	HMEC	breast
25	chr16:65037800-65041600	Strong transcription	NHDF-Ad	bronchial
26	chr16:65037800-65044400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr16:65038200-65040600	Strong transcription	HSMMtube	muscle
28	chr16:65039000-65043600	Weak transcription	Brain Anterior Caudate	brain
29	chr16:65039000-65043800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr16:65039000-65043800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr16:65039000-65061200	Weak transcription	Aorta	Aorta
32	chr16:65039000-65089600	Weak transcription	Fetal Intestine Large	intestine
33	chr16:65039200-65068800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr16:65039400-65040400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr16:65039400-65043600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr16:65039400-65043600	Weak transcription	Fetal Brain Female	brain
37	chr16:65039400-65050800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr16:65039600-65043600	Weak transcription	Brain Germinal Matrix	brain
39	chr16:65039600-65045800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr16:65039600-65049000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr16:65039600-65079800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr16:65039800-65040800	Strong transcription	Placenta	Placenta
43	chr16:65039800-65057400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr16:65040000-65041000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr16:65040000-65041000	Strong transcription	Ovary	ovary
46	chr16:65040000-65044000	Weak transcription	Spleen	Spleen
47	chr16:65040000-65049800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:65040200-65041600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:65040200-65041600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr16:65040200-65045800	Weak transcription	Muscle Satellite Cultured Cells	--

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