SNP Detail Info-rs829642

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

LCLAT1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0287 (8621/29948,GnomAD)
T==0309 (9013/29116,TOPMED)
T==0293 (1465/5008,1000G)
T==0187 (720/3854,ALSPAC)
T==0187 (692/3708,TWINSUK)

Position: chr2:30477104 (GRCh38.p7) (2p23.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 18 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.30477104T>C
GRCh37.p13 chr 2	NC_000002.11:g.30699970T>C

Molecule type	Change	Amino acid[Codon]	SO Term
LCLAT1 transcript variant 2	NM_001002257.2:c.	N/A	Intron Variant
LCLAT1 transcript variant 4	NM_001304445.1:c.	N/A	Intron Variant
LCLAT1 transcript variant 3	NM_001304446.1:c.	N/A	Intron Variant
LCLAT1 transcript variant 1	NM_182551.4:c.	N/A	Intron Variant
LCLAT1 transcript variant X1	XM_005264244.1:c.	N/A	Intron Variant
LCLAT1 transcript variant X3	XM_005264245.3:c.	N/A	Intron Variant
LCLAT1 transcript variant X2	XM_011532741.2:c.	N/A	Intron Variant
LCLAT1 transcript variant X4	XM_011532742.2:c.	N/A	Intron Variant
LCLAT1 transcript variant X6	XM_011532743.2:c.	N/A	Intron Variant
LCLAT1 transcript variant X7	XM_011532744.2:c.	N/A	Intron Variant
LCLAT1 transcript variant X9	XM_011532745.1:c.	N/A	Intron Variant
LCLAT1 transcript variant X5	XM_017003746.1:c.	N/A	Intron Variant
LCLAT1 transcript variant X8	XM_017003747.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.532	C=0.468
1000Genomes	American	Sub	694	T=0.160	C=0.840
1000Genomes	East Asian	Sub	1008	T=0.134	C=0.866
1000Genomes	Europe	Sub	1006	T=0.202	C=0.798
1000Genomes	Global	Study-wide	5008	T=0.293	C=0.707
1000Genomes	South Asian	Sub	978	T=0.320	C=0.680
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.187	C=0.813
The Genome Aggregation Database	African	Sub	8700	T=0.487	C=0.513
The Genome Aggregation Database	American	Sub	838	T=0.130	C=0.870
The Genome Aggregation Database	East Asian	Sub	1618	T=0.136	C=0.864
The Genome Aggregation Database	Europe	Sub	18490	T=0.214	C=0.785
The Genome Aggregation Database	Global	Study-wide	29948	T=0.287	C=0.712
The Genome Aggregation Database	Other	Sub	302	T=0.270	C=0.730
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.309	C=0.690
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.187	C=0.813

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
rs829642	0.000048	alcoholism	pha002892
rs829642	0.000048	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:30699970	LCLAT1	ENSG00000172954.9	T>C	9.0207e-7	29878	Cortex

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	30671494	30671742	E067	-28228
chr2	30669242	30669324	E068	-30646
chr2	30671494	30671742	E068	-28228
chr2	30669242	30669324	E069	-30646
chr2	30671494	30671742	E069	-28228
chr2	30671494	30671742	E070	-28228
chr2	30680492	30680711	E070	-19259
chr2	30680731	30680771	E070	-19199
chr2	30671494	30671742	E072	-28228
chr2	30704086	30704293	E072	4116
chr2	30704376	30704672	E072	4406
chr2	30671494	30671742	E081	-28228
chr2	30715178	30715391	E081	15208
chr2	30715601	30715932	E081	15631
chr2	30671494	30671742	E082	-28228
chr2	30727635	30728044	E082	27665
chr2	30737503	30737708	E082	37533
chr2	30737765	30737887	E082	37795

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	30669469	30671242	E067	-28728
chr2	30669469	30671242	E068	-28728
chr2	30669469	30671242	E069	-28728
chr2	30669469	30671242	E070	-28728
chr2	30669469	30671242	E071	-28728
chr2	30669469	30671242	E072	-28728
chr2	30669469	30671242	E073	-28728
chr2	30669469	30671242	E074	-28728
chr2	30669469	30671242	E081	-28728
chr2	30669469	30671242	E082	-28728

rs829642