SNP Detail Info-rs1251179

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LOC105373612 : Intron Variant
LOC151121 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0482 (14414/29878,GnomAD)
G=0492 (14333/29118,TOPMED)
G=0417 (2087/5008,1000G)
A==0477 (1838/3854,ALSPAC)
A==0492 (1825/3708,TWINSUK)

Position: chr2:129246162 (GRCh38.p7) (2q21.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 20 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.129246162A>G
GRCh37.p13 chr 2	NC_000002.11:g.130003735A>G

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01854 transcript variant 1	NR_122040.1:n.	N/A	Intron Variant
LINC01854 transcript variant 2	NR_122041.1:n.	N/A	Intron Variant
LINC01854 transcript variant 3	NR_122042.1:n.	N/A	Intron Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373612 transcript	XR_001739709.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.548	G=0.452
1000Genomes	American	Sub	694	A=0.560	G=0.440
1000Genomes	East Asian	Sub	1008	A=0.748	G=0.252
1000Genomes	Europe	Sub	1006	A=0.464	G=0.536
1000Genomes	Global	Study-wide	5008	A=0.583	G=0.417
1000Genomes	South Asian	Sub	978	A=0.600	G=0.400
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.477	G=0.523
The Genome Aggregation Database	African	Sub	8694	A=0.535	G=0.465
The Genome Aggregation Database	American	Sub	834	A=0.560	G=0.440
The Genome Aggregation Database	East Asian	Sub	1616	A=0.802	G=0.198
The Genome Aggregation Database	Europe	Sub	18432	A=0.483	G=0.516
The Genome Aggregation Database	Global	Study-wide	29878	A=0.517	G=0.482
The Genome Aggregation Database	Other	Sub	302	A=0.440	G=0.560
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.507	G=0.492
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.492	G=0.508

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
rs1251179	1.25E-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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	129990903	129991022	E070	-12713
chr2	129991443	129991904	E070	-11831
chr2	129990903	129991022	E081	-12713
chr2	129991443	129991904	E081	-11831
chr2	129996773	129997036	E081	-6699
chr2	130010223	130010353	E081	6488
chr2	130010398	130011293	E081	6663
chr2	130038915	130039052	E081	35180
chr2	130039472	130039687	E081	35737
chr2	130039843	130039996	E081	36108
chr2	130050579	130050658	E081	46844
chr2	130050695	130050812	E081	46960
chr2	129996773	129997036	E082	-6699
chr2	130010223	130010353	E082	6488
chr2	130038591	130038845	E082	34856
chr2	130038915	130039052	E082	35180
chr2	130039472	130039687	E082	35737
chr2	130039843	130039996	E082	36108
chr2	130050579	130050658	E082	46844
chr2	130050695	130050812	E082	46960

rs1251179