SNP Detail Info-rs502545

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC107984934 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0339 (10144/29910,GnomAD)
G==0326 (9509/29118,TOPMED)
G==0389 (1950/5008,1000G)
G==0384 (1479/3854,ALSPAC)
G==0387 (1434/3708,TWINSUK)

Position: chr1:29636635 (GRCh38.p7) (1p35.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 55 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.29636635G>A
GRCh37.p13 chr 1	NC_000001.10:g.30109482G>A

Gene: LOC107984934, uncharacterized LOC107984934(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107984934 transcript variant X1	XR_001737956.1:n.	N/A	Intron Variant
LOC107984934 transcript variant X2	XR_001737957.1:n.	N/A	Intron Variant
LOC107984934 transcript variant X3	XR_001737958.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.250	A=0.750
1000Genomes	American	Sub	694	G=0.320	A=0.680
1000Genomes	East Asian	Sub	1008	G=0.507	A=0.493
1000Genomes	Europe	Sub	1006	G=0.394	A=0.606
1000Genomes	Global	Study-wide	5008	G=0.389	A=0.611
1000Genomes	South Asian	Sub	978	G=0.500	A=0.500
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.384	A=0.616
The Genome Aggregation Database	African	Sub	8700	G=0.246	A=0.754
The Genome Aggregation Database	American	Sub	838	G=0.320	A=0.680
The Genome Aggregation Database	East Asian	Sub	1616	G=0.482	A=0.518
The Genome Aggregation Database	Europe	Sub	18454	G=0.370	A=0.629
The Genome Aggregation Database	Global	Study-wide	29910	G=0.339	A=0.660
The Genome Aggregation Database	Other	Sub	302	G=0.390	A=0.610
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.326	A=0.673
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.387	A=0.613

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs502545	0.000556	alcohol consumption (maxi-drinks)	24277619

eQTL of rs502545 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 rs502545 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 )
chr1	30155282	30155336	E067	45800
chr1	30155358	30155428	E067	45876
chr1	30155434	30155490	E067	45952
chr1	30155598	30156126	E067	46116
chr1	30155282	30155336	E068	45800
chr1	30155358	30155428	E068	45876
chr1	30155434	30155490	E068	45952
chr1	30155598	30156126	E068	46116
chr1	30155358	30155428	E069	45876
chr1	30155434	30155490	E069	45952
chr1	30155598	30156126	E069	46116
chr1	30153654	30153787	E070	44172
chr1	30155282	30155336	E070	45800
chr1	30155598	30156126	E070	46116
chr1	30156212	30156306	E070	46730
chr1	30158398	30158458	E070	48916
chr1	30155282	30155336	E071	45800
chr1	30155358	30155428	E071	45876
chr1	30155434	30155490	E071	45952
chr1	30155598	30156126	E071	46116
chr1	30155358	30155428	E072	45876
chr1	30155434	30155490	E072	45952
chr1	30155598	30156126	E072	46116
chr1	30155358	30155428	E074	45876
chr1	30155434	30155490	E074	45952
chr1	30155598	30156126	E074	46116
chr1	30140700	30140863	E081	31218
chr1	30140922	30141874	E081	31440
chr1	30142054	30142152	E081	32572
chr1	30142315	30142408	E081	32833
chr1	30144614	30144827	E081	35132
chr1	30146606	30146850	E081	37124
chr1	30150126	30150335	E081	40644
chr1	30150384	30150434	E081	40902
chr1	30154966	30155068	E081	45484
chr1	30155282	30155336	E081	45800
chr1	30155358	30155428	E081	45876
chr1	30155434	30155490	E081	45952
chr1	30155598	30156126	E081	46116
chr1	30156212	30156306	E081	46730
chr1	30158398	30158458	E081	48916
chr1	30158922	30158994	E081	49440
chr1	30121951	30122292	E082	12469
chr1	30122361	30122706	E082	12879
chr1	30140700	30140863	E082	31218
chr1	30142315	30142408	E082	32833
chr1	30144614	30144827	E082	35132
chr1	30150126	30150335	E082	40644
chr1	30150384	30150434	E082	40902
chr1	30154966	30155068	E082	45484
chr1	30155282	30155336	E082	45800
chr1	30155358	30155428	E082	45876
chr1	30155434	30155490	E082	45952
chr1	30155598	30156126	E082	46116
chr1	30156212	30156306	E082	46730

rs502545