SNP Detail Info-rs4928112

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

TMEM45A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0348 (10415/29890,GnomAD)
A=0328 (9564/29118,TOPMED)
A=0312 (1560/5008,1000G)
A=0433 (1669/3854,ALSPAC)
A=0440 (1631/3708,TWINSUK)

Position: chr3:100544715 (GRCh38.p7) (3q12.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 7 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.100544715G>A
GRCh37.p13 chr 3	NC_000003.11:g.100263559G>A

Molecule type	Change	Amino acid[Codon]	SO Term
TMEM45A transcript	NM_018004.2:c.	N/A	Intron Variant
TMEM45A transcript variant X1	XM_005247569.2:c.	N/A	Intron Variant
TMEM45A transcript variant X2	XM_017006715.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.784	A=0.216
1000Genomes	American	Sub	694	G=0.620	A=0.380
1000Genomes	East Asian	Sub	1008	G=0.682	A=0.318
1000Genomes	Europe	Sub	1006	G=0.562	A=0.438
1000Genomes	Global	Study-wide	5008	G=0.688	A=0.312
1000Genomes	South Asian	Sub	978	G=0.740	A=0.260
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	8710	G=0.790	A=0.210
The Genome Aggregation Database	American	Sub	834	G=0.530	A=0.470
The Genome Aggregation Database	East Asian	Sub	1612	G=0.695	A=0.305
The Genome Aggregation Database	Europe	Sub	18434	G=0.591	A=0.408
The Genome Aggregation Database	Global	Study-wide	29890	G=0.651	A=0.348
The Genome Aggregation Database	Other	Sub	300	G=0.460	A=0.540
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.671	A=0.328
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.560	A=0.440

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

SNP ID	p-value	Traits	Study
rs4928112	0.000224	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr3:100263559	TMEM45A	ENSG00000181458.6	G>A	1.1104e-3	52096	Substantia_nigra

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr3	100251385	100251599	E069	-11960
chr3	100251385	100251599	E070	-11960
chr3	100252039	100252352	E070	-11207
chr3	100252699	100252749	E070	-10810
chr3	100253608	100253817	E070	-9742
chr3	100251385	100251599	E071	-11960
chr3	100251385	100251599	E074	-11960

rs4928112