SNP Detail Info-rs4673925

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ABCA12 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0494 (59769/120792,ExAC)
A==0490 (14643/29866,GnomAD)
A==0480 (13988/29118,TOPMED)
G=0486 (6328/13004,GO-ESP)
G=0458 (2292/5008,1000G)
G=0498 (1921/3854,ALSPAC)
A==0487 (1805/3708,TWINSUK)

Position: chr2:214968691 (GRCh38.p7) (2q35)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 14 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.214968691A>G
GRCh37.p13 chr 2	NC_000002.11:g.215833415A>G
ABCA12 RefSeqGene	NG_007074.1:g.174737T>C

Gene: ABCA12, ATP binding cassette subfamily A member 12(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ABCA12 transcript variant 2	NM_015657.3:c.	N/A	Intron Variant
ABCA12 transcript variant 1	NM_173076.2:c.	N/A	Intron Variant
ABCA12 transcript variant 3	NR_103740.1:n.	N/A	Intron Variant
ABCA12 transcript variant X1	XM_011510951.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.465	G=0.535
1000Genomes	American	Sub	694	A=0.480	G=0.520
1000Genomes	East Asian	Sub	1008	A=0.749	G=0.251
1000Genomes	Europe	Sub	1006	A=0.513	G=0.487
1000Genomes	Global	Study-wide	5008	A=0.542	G=0.458
1000Genomes	South Asian	Sub	978	A=0.510	G=0.490
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.502	G=0.498
The Exome Aggregation Consortium	American	Sub	21664	A=0.466	G=0.533
The Exome Aggregation Consortium	Asian	Sub	25068	A=0.576	G=0.423
The Exome Aggregation Consortium	Europe	Sub	73156	A=0.475	G=0.524
The Exome Aggregation Consortium	Global	Study-wide	120792	A=0.494	G=0.505
The Exome Aggregation Consortium	Other	Sub	904	A=0.500	G=0.500
The Genome Aggregation Database	African	Sub	8692	A=0.490	G=0.510
The Genome Aggregation Database	American	Sub	836	A=0.480	G=0.520
The Genome Aggregation Database	East Asian	Sub	1610	A=0.729	G=0.271
The Genome Aggregation Database	Europe	Sub	18426	A=0.469	G=0.530
The Genome Aggregation Database	Global	Study-wide	29866	A=0.490	G=0.509
The Genome Aggregation Database	Other	Sub	302	A=0.500	G=0.500
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.480	G=0.519
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.487	G=0.513

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
rs4673925	0.00035	alcohol dependence	20201924

eQTL of rs4673925 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 rs4673925 in Fetal Brain

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

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	215867838	215868029	E067	34423
chr2	215867223	215867698	E068	33808
chr2	215867838	215868029	E068	34423
chr2	215867223	215867698	E070	33808
chr2	215867838	215868029	E070	34423
chr2	215867223	215867698	E072	33808
chr2	215867838	215868029	E072	34423
chr2	215867223	215867698	E073	33808
chr2	215867838	215868029	E073	34423
chr2	215867223	215867698	E081	33808
chr2	215867838	215868029	E081	34423
chr2	215867223	215867698	E082	33808
chr2	215867838	215868029	E082	34423
chr2	215870072	215870178	E082	36657

rs4673925