rs11608979

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

TMEM132C : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0388 (11642/29932,GnomAD)
A=0359 (10463/29118,TOPMED)
A=0375 (1880/5008,1000G)
A=0433 (1670/3854,ALSPAC)
A=0431 (1597/3708,TWINSUK)

Position: chr12:128677080 (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.128677080G>A
GRCh37.p13 chr 12	NC_000012.11:g.129161625G>A

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=0.754	A=0.246
1000Genomes	American	Sub	694	G=0.610	A=0.390
1000Genomes	East Asian	Sub	1008	G=0.601	A=0.399
1000Genomes	Europe	Sub	1006	G=0.561	A=0.439
1000Genomes	Global	Study-wide	5008	G=0.625	A=0.375
1000Genomes	South Asian	Sub	978	G=0.550	A=0.450
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.567	A=0.433
The Genome Aggregation Database	African	Sub	8706	G=0.730	A=0.270
The Genome Aggregation Database	American	Sub	838	G=0.630	A=0.370
The Genome Aggregation Database	East Asian	Sub	1612	G=0.583	A=0.417
The Genome Aggregation Database	Europe	Sub	18474	G=0.556	A=0.443
The Genome Aggregation Database	Global	Study-wide	29932	G=0.611	A=0.388
The Genome Aggregation Database	Other	Sub	302	G=0.620	A=0.380
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.640	A=0.359
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.569	A=0.431

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
rs11608979	0.00015	alcohol dependence(early age of onset)	20201924
rs11608979	0.00017	alcohol dependence	20201924

eQTL of rs11608979 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 rs11608979 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	-24751
chr12	129169006	129169234	E067	7381
chr12	129169242	129169363	E067	7617
chr12	129169485	129169535	E067	7860
chr12	129176616	129176696	E067	14991
chr12	129176885	129176945	E067	15260
chr12	129199266	129199327	E067	37641
chr12	129169006	129169234	E068	7381
chr12	129169242	129169363	E068	7617
chr12	129169485	129169535	E068	7860
chr12	129169673	129169723	E068	8048
chr12	129127406	129127495	E069	-34130
chr12	129127653	129127861	E069	-33764
chr12	129127892	129128114	E069	-33511
chr12	129136834	129136874	E069	-24751
chr12	129138683	129138754	E069	-22871
chr12	129138761	129138821	E069	-22804
chr12	129139125	129139282	E069	-22343
chr12	129145681	129146264	E069	-15361
chr12	129169006	129169234	E069	7381
chr12	129169242	129169363	E069	7617
chr12	129169485	129169535	E069	7860
chr12	129169673	129169723	E069	8048
chr12	129175392	129175442	E069	13767
chr12	129136834	129136874	E070	-24751
chr12	129138761	129138821	E070	-22804
chr12	129139125	129139282	E070	-22343
chr12	129144617	129144691	E070	-16934
chr12	129144929	129145350	E070	-16275
chr12	129145681	129146264	E070	-15361
chr12	129146497	129146687	E070	-14938
chr12	129146715	129146969	E070	-14656
chr12	129147088	129147275	E070	-14350
chr12	129127406	129127495	E071	-34130
chr12	129127892	129128114	E071	-33511
chr12	129134540	129134618	E071	-27007
chr12	129134677	129134726	E071	-26899
chr12	129137551	129137601	E071	-24024
chr12	129137796	129137874	E071	-23751
chr12	129137897	129137947	E071	-23678
chr12	129138155	129138249	E071	-23376
chr12	129169006	129169234	E071	7381
chr12	129169242	129169363	E071	7617
chr12	129169485	129169535	E071	7860
chr12	129169673	129169723	E071	8048
chr12	129200078	129200279	E071	38453
chr12	129136834	129136874	E072	-24751
chr12	129137551	129137601	E072	-24024
chr12	129138761	129138821	E072	-22804
chr12	129169006	129169234	E072	7381
chr12	129169242	129169363	E072	7617
chr12	129169006	129169234	E073	7381
chr12	129169242	129169363	E073	7617
chr12	129169485	129169535	E073	7860
chr12	129172475	129172620	E073	10850
chr12	129172745	129172795	E073	11120
chr12	129169006	129169234	E074	7381
chr12	129169242	129169363	E074	7617
chr12	129169485	129169535	E074	7860
chr12	129127892	129128114	E081	-33511
chr12	129145681	129146264	E081	-15361
chr12	129169006	129169234	E081	7381
chr12	129183532	129183605	E081	21907