SNP Detail Info-rs4886227

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

TDRD3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0147 (4428/29938,GnomAD)
G=0134 (3926/29116,TOPMED)
G=0174 (869/5008,1000G)
G=0164 (631/3854,ALSPAC)
G=0176 (651/3708,TWINSUK)

Position: chr13:60416372 (GRCh38.p7) (13q21.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 12 Enhancers around

Promoter: 14 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 13	NC_000013.11:g.60416372A>G
GRCh37.p13 chr 13	NC_000013.10:g.60990506A>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 X5	XM_017020777.1:c.	N/A	Intron Variant
TDRD3 transcript variant X1	XM_011535247.1:c.	N/A	Genic Upstream Transcript Variant
TDRD3 transcript variant X7	XM_011535249.2:c.	N/A	Genic Upstream Transcript Variant
TDRD3 transcript variant X3	XR_941666.2:n.	N/A	Genic Upstream Transcript Variant
TDRD3 transcript variant X4	XR_941667.1:n.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.923	G=0.077
1000Genomes	American	Sub	694	A=0.670	G=0.330
1000Genomes	East Asian	Sub	1008	A=0.785	G=0.215
1000Genomes	Europe	Sub	1006	A=0.866	G=0.134
1000Genomes	Global	Study-wide	5008	A=0.826	G=0.174
1000Genomes	South Asian	Sub	978	A=0.810	G=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.836	G=0.164
The Genome Aggregation Database	African	Sub	8720	A=0.913	G=0.087
The Genome Aggregation Database	American	Sub	836	A=0.710	G=0.290
The Genome Aggregation Database	East Asian	Sub	1612	A=0.778	G=0.222
The Genome Aggregation Database	Europe	Sub	18468	A=0.836	G=0.164
The Genome Aggregation Database	Global	Study-wide	29938	A=0.852	G=0.147
The Genome Aggregation Database	Other	Sub	302	A=0.860	G=0.140
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.865	G=0.134
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.824	G=0.176

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
rs4886227	0.00015	alcohol dependence(early age of onset)	20201924
rs4886227	0.0003	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	60973646	60973749	E067	-16757
chr13	60973753	60973845	E067	-16661
chr13	60987505	60987654	E067	-2852
chr13	60973646	60973749	E068	-16757
chr13	60973753	60973845	E068	-16661
chr13	60973929	60973987	E068	-16519
chr13	60984072	60984945	E068	-5561
chr13	60985614	60985699	E068	-4807
chr13	60985708	60985791	E068	-4715
chr13	60985807	60985921	E068	-4585
chr13	60975875	60976022	E069	-14484
chr13	60984072	60984945	E071	-5561

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr13	60969611	60969651	E067	-20855
chr13	60969674	60969781	E067	-20725
chr13	60969821	60973640	E067	-16866
chr13	60969821	60973640	E068	-16866
chr13	60969821	60973640	E069	-16866
chr13	60969821	60973640	E070	-16866
chr13	60969821	60973640	E071	-16866
chr13	60969611	60969651	E072	-20855
chr13	60969674	60969781	E072	-20725
chr13	60969821	60973640	E072	-16866
chr13	60969821	60973640	E073	-16866
chr13	60969821	60973640	E074	-16866
chr13	60969821	60973640	E081	-16866
chr13	60969821	60973640	E082	-16866

rs4886227