SNP Detail Info-rs5754638

Organism: Homo sapiens

Alleles: A>G / A>T

Gene : Feature

LARGE : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0096 (2899/29970,GnomAD)
T=0072 (360/5008,1000G)
T=0134 (516/3854,ALSPAC)
T=0156 (579/3708,TWINSUK)

Position: chr22:33682071 (GRCh38.p7) (22q12.3)

Phenotype: AD

Dataset:

GWASdb2 | GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Molecule type	Change	Amino acid[Codon]	SO Term
LARGE1 transcript variant 1	NM_004737.4:c.	N/A	Intron Variant
LARGE1 transcript variant 2	NM_133642.3:c.	N/A	Intron Variant
LARGE1 transcript variant X1	XM_005261831.3:c.	N/A	Intron Variant
LARGE1 transcript variant X3	XM_005261832.3:c.	N/A	Intron Variant
LARGE1 transcript variant X2	XM_011530510.2:c.	N/A	Intron Variant
LARGE transcript variant X7	XM_011530514.2:c.	N/A	Intron Variant
LARGE1 transcript variant X6	XM_011530512.2:c.	N/A	Genic Upstream Transcript Variant
LARGE1 transcript variant X7	XM_011530513.2:c.	N/A	Genic Upstream Transcript Variant
LARGE transcript variant X4	XR_001755370.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.994	T=0.006
1000Genomes	American	Sub	694	A=0.860	T=0.140
1000Genomes	East Asian	Sub	1008	A=0.918	T=0.082
1000Genomes	Europe	Sub	1006	A=0.897	T=0.103
1000Genomes	Global	Study-wide	5008	A=0.928	T=0.072
1000Genomes	South Asian	Sub	978	A=0.930	T=0.070
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.866	T=0.134
The Genome Aggregation Database	African	Sub	8728	A=0.976	T=0.024
The Genome Aggregation Database	American	Sub	838	A=0.900	T=0.100
The Genome Aggregation Database	East Asian	Sub	1618	A=0.927	T=0.073
The Genome Aggregation Database	Europe	Sub	18484	A=0.866	T=0.133
The Genome Aggregation Database	Global	Study-wide	29970	A=0.903	T=0.096
The Genome Aggregation Database	Other	Sub	302	A=0.960	T=0.040
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.844	T=0.156

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

SNP ID	p-value	Traits	Study
rs5754638	8E-06	alcohol dependence (age at onset)	24962325

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

rs5754638