SNP Detail Info-rs4534007

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LAMA2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0490 (14536/29644,GnomAD)
A=0438 (12777/29118,TOPMED)
G==0450 (2252/5008,1000G)
G==0409 (1575/3854,ALSPAC)
G==0419 (1554/3708,TWINSUK)

Position: chr6:129052544 (GRCh38.p7) (6q22.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 9 Enhancers around

Promoter: 0 Promoter around

Molecule type	Change	Amino acid[Codon]	SO Term
LAMA2 transcript variant 1	NM_000426.3:c.	N/A	Intron Variant
LAMA2 transcript variant 2	NM_001079823.1:c.	N/A	Intron Variant
LAMA2 transcript variant X1	XM_005266981.3:c.	N/A	Intron Variant
LAMA2 transcript variant X3	XM_005266982.3:c.	N/A	Intron Variant
LAMA2 transcript variant X2	XM_011535820.2:c.	N/A	Intron Variant
LAMA2 transcript variant X4	XM_017010851.1:c.	N/A	Intron Variant
LAMA2 transcript variant X6	XM_017010853.1:c.	N/A	Intron Variant
LAMA2 transcript variant X5	XM_017010852.1:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.780	A=0.220
1000Genomes	American	Sub	694	G=0.340	A=0.660
1000Genomes	East Asian	Sub	1008	G=0.169	A=0.831
1000Genomes	Europe	Sub	1006	G=0.439	A=0.561
1000Genomes	Global	Study-wide	5008	G=0.450	A=0.550
1000Genomes	South Asian	Sub	978	G=0.380	A=0.620
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.409	A=0.591
The Genome Aggregation Database	African	Sub	8686	G=0.746	A=0.254
The Genome Aggregation Database	American	Sub	834	G=0.290	A=0.710
The Genome Aggregation Database	East Asian	Sub	1610	G=0.191	A=0.809
The Genome Aggregation Database	Europe	Sub	18212	G=0.403	A=0.597
The Genome Aggregation Database	Global	Study-wide	29644	G=0.490	A=0.509
The Genome Aggregation Database	Other	Sub	302	G=0.560	A=0.440
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.561	A=0.438
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.419	A=0.581

PMID	Title	Author	Journal
19581569	Genome-wide association study of alcohol dependence.	Treutlein J	Arch Gen Psychiatry

SNP ID	p-value	Traits	Study
rs4534007	7.23E-05	alcohol dependence	19581569

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 )
chr6	129415073	129415166	E068	41384
chr6	129415073	129415166	E069	41384
chr6	129415230	129415702	E069	41541
chr6	129415073	129415166	E071	41384
chr6	129415230	129415702	E071	41541
chr6	129328003	129328272	E074	-45417
chr6	129328294	129328358	E074	-45331
chr6	129346564	129346614	E081	-27075
chr6	129346815	129346927	E081	-26762

rs4534007