SNP Detail Info-rs1464678

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ABCA12 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0498 (14896/29878,GnomAD)
A==0494 (14404/29118,TOPMED)
G=0453 (2268/5008,1000G)
G=0499 (1922/3854,ALSPAC)
A==0486 (1802/3708,TWINSUK)

Position: chr2:214969742 (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

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

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.502	G=0.498
1000Genomes	American	Sub	694	A=0.490	G=0.510
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=0.547	G=0.453
1000Genomes	South Asian	Sub	978	A=0.480	G=0.520
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.501	G=0.499
The Genome Aggregation Database	African	Sub	8698	A=0.518	G=0.482
The Genome Aggregation Database	American	Sub	836	A=0.480	G=0.520
The Genome Aggregation Database	East Asian	Sub	1616	A=0.735	G=0.265
The Genome Aggregation Database	Europe	Sub	18428	A=0.469	G=0.530
The Genome Aggregation Database	Global	Study-wide	29878	A=0.498	G=0.501
The Genome Aggregation Database	Other	Sub	300	A=0.510	G=0.490
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.494	G=0.505
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.486	G=0.514

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
rs1464678	0.00025	alcohol dependence	20201924

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

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	215867838	215868029	E067	33372
chr2	215867223	215867698	E068	32757
chr2	215867838	215868029	E068	33372
chr2	215867223	215867698	E070	32757
chr2	215867838	215868029	E070	33372
chr2	215867223	215867698	E072	32757
chr2	215867838	215868029	E072	33372
chr2	215867223	215867698	E073	32757
chr2	215867838	215868029	E073	33372
chr2	215867223	215867698	E081	32757
chr2	215867838	215868029	E081	33372
chr2	215867223	215867698	E082	32757
chr2	215867838	215868029	E082	33372
chr2	215870072	215870178	E082	35606

rs1464678