SNP Detail Info-rs4952147

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LCLAT1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0299 (8956/29930,GnomAD)
G==0328 (9575/29116,TOPMED)
G==0303 (1517/5008,1000G)
G==0184 (708/3854,ALSPAC)
G==0185 (685/3708,TWINSUK)

Position: chr2:30553404 (GRCh38.p7) (2p23.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 10 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.30553404G>A
GRCh37.p13 chr 2	NC_000002.11:g.30776270G>A

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 X5	XM_017003746.1:c.	N/A	Intron Variant
LCLAT1 transcript variant X8	XM_017003747.1:c.	N/A	Intron Variant
LCLAT1 transcript variant X9	XM_011532745.1:c.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.587	A=0.413
1000Genomes	American	Sub	694	G=0.160	A=0.840
1000Genomes	East Asian	Sub	1008	G=0.136	A=0.864
1000Genomes	Europe	Sub	1006	G=0.194	A=0.806
1000Genomes	Global	Study-wide	5008	G=0.303	A=0.697
1000Genomes	South Asian	Sub	978	G=0.300	A=0.700
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.184	A=0.816
The Genome Aggregation Database	African	Sub	8702	G=0.534	A=0.466
The Genome Aggregation Database	American	Sub	836	G=0.130	A=0.870
The Genome Aggregation Database	East Asian	Sub	1622	G=0.137	A=0.863
The Genome Aggregation Database	Europe	Sub	18468	G=0.211	A=0.788
The Genome Aggregation Database	Global	Study-wide	29930	G=0.299	A=0.700
The Genome Aggregation Database	Other	Sub	302	G=0.270	A=0.730
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.328	A=0.671
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.185	A=0.815

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
rs4952147	0.00022	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:30776270	LCLAT1	ENSG00000172954.9	G>A	9.0207e-7	106178	Cortex

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	30752501	30752624	E068	-23646
chr2	30806133	30806402	E069	29863
chr2	30806446	30806504	E069	30176
chr2	30796195	30796333	E070	19925
chr2	30796351	30796423	E070	20081
chr2	30797251	30797578	E074	20981
chr2	30797690	30797969	E074	21420
chr2	30727635	30728044	E082	-48226
chr2	30737503	30737708	E082	-38562
chr2	30737765	30737887	E082	-38383

rs4952147