Variant report

Variant	rs12708869
Chromosome Location	chr16:65057323-65057324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1025312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11640810	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11647164	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	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12923516	0.81[EUR][1000 genomes]
rs1520233	0.87[GIH][hapmap]
rs1607696	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1826821	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs185393	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2280394	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs2331446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2860056	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35141	0.86[JPT][hapmap]
rs35143	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs35153	0.82[ASN][1000 genomes]
rs35181	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs35183	0.95[ASN][1000 genomes]
rs35184	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs35186	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs35187	0.95[ASN][1000 genomes]
rs35190	0.95[ASN][1000 genomes]
rs35197	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs3760056	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]
rs3826240	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4967879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4967881	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7195682	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs973199	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9930786	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12708869	CMTM1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:65039000-65061200	Weak transcription	Aorta	Aorta
2	chr16:65039000-65089600	Weak transcription	Fetal Intestine Large	intestine
3	chr16:65039200-65068800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:65039600-65079800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr16:65039800-65057400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr16:65040600-65086000	Weak transcription	HMEC	breast
7	chr16:65041000-65059200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:65041200-65072400	Weak transcription	Fetal Kidney	kidney
9	chr16:65044600-65064000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr16:65044600-65069000	Weak transcription	Brain Germinal Matrix	brain
11	chr16:65046400-65075600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr16:65047200-65058800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr16:65047200-65059000	Weak transcription	HSMMtube	muscle
14	chr16:65047200-65061200	Weak transcription	NHLF	lung
15	chr16:65047200-65078400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr16:65047400-65058800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr16:65050800-65061200	Weak transcription	Brain Anterior Caudate	brain
18	chr16:65051000-65062400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr16:65051000-65071200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr16:65051200-65062600	Weak transcription	Brain Hippocampus Middle	brain
21	chr16:65051200-65062600	Weak transcription	Brain Substantia Nigra	brain
22	chr16:65051200-65063400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr16:65051200-65063400	Weak transcription	Fetal Brain Male	brain
24	chr16:65052200-65070800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr16:65052800-65058600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr16:65052800-65068800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr16:65053000-65062000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr16:65053000-65065000	Weak transcription	HSMM	muscle
29	chr16:65053000-65065200	Weak transcription	NHDF-Ad	bronchial
30	chr16:65053000-65069000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr16:65053800-65057400	Weak transcription	HUVEC	blood vessel
32	chr16:65056400-65057800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr16:65056400-65057800	Strong transcription	Fetal Lung	lung
34	chr16:65056400-65058000	Genic enhancers	Ovary	ovary
35	chr16:65056600-65057600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr16:65056600-65057800	Strong transcription	Osteobl	bone
37	chr16:65056600-65061400	Weak transcription	Fetal Muscle Leg	muscle
38	chr16:65056800-65058000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr16:65056800-65058000	Strong transcription	Fetal Stomach	stomach
40	chr16:65056800-65072800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr16:65057000-65057800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr16:65057000-65057800	Strong transcription	NH-A	brain
43	chr16:65057200-65058200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links