SNP Detail Info-rs12865240

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

TDRD3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0124 (3719/29942,GnomAD)
G=0106 (3091/29116,TOPMED)
G=0130 (651/5008,1000G)
G=0162 (626/3854,ALSPAC)
G=0175 (649/3708,TWINSUK)

Position: chr13:60545223 (GRCh38.p7) (13q21.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 2 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 13	NC_000013.11:g.60545223A>G
GRCh37.p13 chr 13	NC_000013.10:g.61119357A>G

Molecule type	Change	Amino acid[Codon]	SO Term
TDRD3 transcript variant 1	NM_001146070.1:c.	N/A	Intron Variant
TDRD3 transcript variant 3	NM_001146071.1:c.	N/A	Intron Variant
TDRD3 transcript variant 2	NM_030794.2:c.	N/A	Intron Variant
TDRD3 transcript variant X2	XM_005266556.4:c.	N/A	Intron Variant
TDRD3 transcript variant X7	XM_005266560.2:c.	N/A	Intron Variant
TDRD3 transcript variant X1	XM_011535247.1:c.	N/A	Intron Variant
TDRD3 transcript variant X5	XM_017020777.1:c.	N/A	Intron Variant
TDRD3 transcript variant X7	XM_011535249.2:c.	N/A	Genic Downstream Transcript Variant
TDRD3 transcript variant X3	XR_941666.2:n.	N/A	Intron Variant
TDRD3 transcript variant X4	XR_941667.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.971	G=0.029
1000Genomes	American	Sub	694	A=0.820	G=0.180
1000Genomes	East Asian	Sub	1008	A=0.816	G=0.184
1000Genomes	Europe	Sub	1006	A=0.875	G=0.125
1000Genomes	Global	Study-wide	5008	A=0.870	G=0.130
1000Genomes	South Asian	Sub	978	A=0.820	G=0.180
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.838	G=0.162
The Genome Aggregation Database	African	Sub	8728	A=0.959	G=0.041
The Genome Aggregation Database	American	Sub	838	A=0.870	G=0.130
The Genome Aggregation Database	East Asian	Sub	1614	A=0.796	G=0.204
The Genome Aggregation Database	Europe	Sub	18460	A=0.843	G=0.156
The Genome Aggregation Database	Global	Study-wide	29942	A=0.875	G=0.124
The Genome Aggregation Database	Other	Sub	302	A=0.870	G=0.130
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.893	G=0.106
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.825	G=0.175

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
rs12865240	0.00073	alcohol dependence(early age of onset)	20201924
rs12865240	0.00085	alcohol dependence	20201924

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 )
chr13	61165031	61165878	E081	45674
chr13	61166228	61166278	E081	46871

rs12865240