Variant report

Variant	rs1520233
Chromosome Location	chr16:65088392-65088393
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11640810	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs11647164	0.87[GIH][hapmap];0.82[MEX][hapmap]
rs12708869	0.87[GIH][hapmap]
rs12923000	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1554400	0.81[ASN][1000 genomes]
rs1826821	0.80[EUR][1000 genomes]
rs2331446	0.87[GIH][hapmap]
rs2860056	0.80[EUR][1000 genomes]
rs3760056	0.87[GIH][hapmap];0.82[MEX][hapmap]
rs4967879	0.87[GIH][hapmap];0.82[MEX][hapmap]
rs4967883	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs765771	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9930786	0.87[GIH][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv833260	chr16:65050647-65218759	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1831	chr16:65071976-65106105	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1520233	CMTM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:65039000-65089600	Weak transcription	Fetal Intestine Large	intestine
2	chr16:65058600-65104400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr16:65069800-65105000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr16:65072800-65088800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr16:65072800-65096200	Weak transcription	Colon Smooth Muscle	Colon
6	chr16:65074400-65094000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr16:65079000-65093000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr16:65080200-65091000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:65080400-65088600	Weak transcription	Spleen	Spleen
10	chr16:65080400-65088800	Weak transcription	Fetal Brain Male	brain
11	chr16:65081200-65088400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr16:65081800-65094800	Weak transcription	Lung	lung
13	chr16:65082800-65093200	Strong transcription	NH-A	brain
14	chr16:65083400-65088400	Strong transcription	Fetal Kidney	kidney
15	chr16:65083800-65100000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr16:65085000-65095800	Weak transcription	Fetal Brain Female	brain
17	chr16:65085400-65089000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:65087400-65088600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr16:65087400-65104800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr16:65087600-65089200	Weak transcription	Brain Germinal Matrix	brain
21	chr16:65087800-65088400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr16:65087800-65088400	Weak transcription	Brain Hippocampus Middle	brain
23	chr16:65087800-65088600	Weak transcription	Fetal Stomach	stomach
24	chr16:65087800-65089000	Weak transcription	Fetal Muscle Leg	muscle
25	chr16:65087800-65090400	Weak transcription	HMEC	breast
26	chr16:65087800-65091000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr16:65087800-65100600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr16:65087800-65102000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr16:65087800-65103600	Weak transcription	Aorta	Aorta
30	chr16:65088000-65088600	Enhancers	Brain Substantia Nigra	brain
31	chr16:65088000-65089000	Genic enhancers	Osteobl	bone
32	chr16:65088000-65089200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:65088000-65089200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr16:65088000-65089600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr16:65088000-65089600	Genic enhancers	HSMM	muscle
36	chr16:65088000-65091200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr16:65088000-65093800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr16:65088000-65095600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr16:65088200-65088400	Genic enhancers	Ovary	ovary
40	chr16:65088200-65088600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr16:65088200-65088800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr16:65088200-65089200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr16:65088200-65089200	Genic enhancers	Fetal Lung	lung
44	chr16:65088200-65089200	Enhancers	NHDF-Ad	bronchial
45	chr16:65088200-65089200	Enhancers	NHLF	lung
46	chr16:65088200-65089600	Enhancers	Brain Angular Gyrus	brain
47	chr16:65088200-65089600	Enhancers	HSMMtube	muscle
48	chr16:65088200-65091000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr16:65088200-65093200	Enhancers	Brain Anterior Caudate	brain
50	chr16:65088200-65101600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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