rs10773566

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

TMEM132C : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0380 (11391/29932,GnomAD)
G==0342 (9984/29118,TOPMED)
G==0341 (1709/5008,1000G)
G==0448 (1725/3854,ALSPAC)
G==0450 (1669/3708,TWINSUK)

Position: chr12:128679103 (GRCh38.p7) (12q24.32)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 63 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.128679103G>T
GRCh37.p13 chr 12	NC_000012.11:g.129163648G>T

Gene: TMEM132C, transmembrane protein 132C(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMEM132C transcript	NM_001136103.2:c.	N/A	Intron Variant
TMEM132C transcript variant X1	XM_011538998.2:c.	N/A	Intron Variant
TMEM132C transcript variant X2	XR_001748922.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.139	T=0.861
1000Genomes	American	Sub	694	G=0.430	T=0.570
1000Genomes	East Asian	Sub	1008	G=0.378	T=0.622
1000Genomes	Europe	Sub	1006	G=0.441	T=0.559
1000Genomes	Global	Study-wide	5008	G=0.341	T=0.659
1000Genomes	South Asian	Sub	978	G=0.410	T=0.590
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.448	T=0.552
The Genome Aggregation Database	African	Sub	8724	G=0.203	T=0.797
The Genome Aggregation Database	American	Sub	834	G=0.430	T=0.570
The Genome Aggregation Database	East Asian	Sub	1622	G=0.406	T=0.594
The Genome Aggregation Database	Europe	Sub	18450	G=0.459	T=0.540
The Genome Aggregation Database	Global	Study-wide	29932	G=0.380	T=0.619
The Genome Aggregation Database	Other	Sub	302	G=0.440	T=0.560
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.342	T=0.657
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.450	T=0.550

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs10773566	0.0000168	alcoholism	pha002893
rs10773566	0.000017	alcohol dependence	20201924
rs10773566	0.000075	alcohol dependence(early age of onset)	20201924
rs10773566	0.0000752	alcoholism	pha002892

eQTL of rs10773566 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs10773566 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr12	129136834	129136874	E067	-26774
chr12	129169006	129169234	E067	5358
chr12	129169242	129169363	E067	5594
chr12	129169485	129169535	E067	5837
chr12	129176616	129176696	E067	12968
chr12	129176885	129176945	E067	13237
chr12	129199266	129199327	E067	35618
chr12	129169006	129169234	E068	5358
chr12	129169242	129169363	E068	5594
chr12	129169485	129169535	E068	5837
chr12	129169673	129169723	E068	6025
chr12	129127406	129127495	E069	-36153
chr12	129127653	129127861	E069	-35787
chr12	129127892	129128114	E069	-35534
chr12	129136834	129136874	E069	-26774
chr12	129138683	129138754	E069	-24894
chr12	129138761	129138821	E069	-24827
chr12	129139125	129139282	E069	-24366
chr12	129145681	129146264	E069	-17384
chr12	129169006	129169234	E069	5358
chr12	129169242	129169363	E069	5594
chr12	129169485	129169535	E069	5837
chr12	129169673	129169723	E069	6025
chr12	129175392	129175442	E069	11744
chr12	129136834	129136874	E070	-26774
chr12	129138761	129138821	E070	-24827
chr12	129139125	129139282	E070	-24366
chr12	129144617	129144691	E070	-18957
chr12	129144929	129145350	E070	-18298
chr12	129145681	129146264	E070	-17384
chr12	129146497	129146687	E070	-16961
chr12	129146715	129146969	E070	-16679
chr12	129147088	129147275	E070	-16373
chr12	129127406	129127495	E071	-36153
chr12	129127892	129128114	E071	-35534
chr12	129134540	129134618	E071	-29030
chr12	129134677	129134726	E071	-28922
chr12	129137551	129137601	E071	-26047
chr12	129137796	129137874	E071	-25774
chr12	129137897	129137947	E071	-25701
chr12	129138155	129138249	E071	-25399
chr12	129169006	129169234	E071	5358
chr12	129169242	129169363	E071	5594
chr12	129169485	129169535	E071	5837
chr12	129169673	129169723	E071	6025
chr12	129200078	129200279	E071	36430
chr12	129136834	129136874	E072	-26774
chr12	129137551	129137601	E072	-26047
chr12	129138761	129138821	E072	-24827
chr12	129169006	129169234	E072	5358
chr12	129169242	129169363	E072	5594
chr12	129169006	129169234	E073	5358
chr12	129169242	129169363	E073	5594
chr12	129169485	129169535	E073	5837
chr12	129172475	129172620	E073	8827
chr12	129172745	129172795	E073	9097
chr12	129169006	129169234	E074	5358
chr12	129169242	129169363	E074	5594
chr12	129169485	129169535	E074	5837
chr12	129127892	129128114	E081	-35534
chr12	129145681	129146264	E081	-17384
chr12	129169006	129169234	E081	5358
chr12	129183532	129183605	E081	19884