SNP Detail Info-rs16854429

Organism: Homo sapiens

Alleles: G>C / G>T

Gene : Feature

TDRD5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0213 (25885/121324,ExAC)
T=0179 (5378/29944,GnomAD)
T=0151 (4402/29118,TOPMED)
G==0168 (2192/13006,GO-ESP)
T=0220 (1103/5008,1000G)
T=0212 (816/3854,ALSPAC)
T=0220 (814/3708,TWINSUK)

Position: chr1:179640454 (GRCh38.p7) (1q25.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 7 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.179640454G>C
GRCh38.p7 chr 1	NC_000001.11:g.179640454G>T
GRCh37.p13 chr 1	NC_000001.10:g.179609589G>C
GRCh37.p13 chr 1	NC_000001.10:g.179609589G>T

Gene: TDRD5, tudor domain containing 5(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TDRD5 transcript variant 1	NM_001199085.1:c.	N/A	Intron Variant
TDRD5 transcript variant 2	NM_001199089.1:c.	N/A	Intron Variant
TDRD5 transcript variant 4	NM_001199091.1:c.	N/A	Intron Variant
TDRD5 transcript variant 5	NM_001199092.1:c.	N/A	Intron Variant
TDRD5 transcript variant 3	NM_173533.3:c.	N/A	Intron Variant
TDRD5 transcript variant X1	XM_005244934.1:c.	N/A	Intron Variant
TDRD5 transcript variant X2	XM_005244935.4:c.	N/A	Intron Variant
TDRD5 transcript variant X3	XM_017000473.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.918	T=0.082
1000Genomes	American	Sub	694	G=0.750	T=0.250
1000Genomes	East Asian	Sub	1008	G=0.645	T=0.355
1000Genomes	Europe	Sub	1006	G=0.788	T=0.212
1000Genomes	Global	Study-wide	5008	G=0.780	T=0.220
1000Genomes	South Asian	Sub	978	G=0.750	T=0.250
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.788	T=0.212
The Exome Aggregation Consortium	American	Sub	21968	G=0.824	T=0.176
The Exome Aggregation Consortium	Asian	Sub	25140	G=0.705	T=0.294
The Exome Aggregation Consortium	Europe	Sub	73310	G=0.803	T=0.197
The Exome Aggregation Consortium	Global	Study-wide	121324	G=0.786	T=0.213
The Exome Aggregation Consortium	Other	Sub	906	G=0.810	T=0.190
The Genome Aggregation Database	African	Sub	8720	G=0.910	T=0.090
The Genome Aggregation Database	American	Sub	838	G=0.770	T=0.230
The Genome Aggregation Database	East Asian	Sub	1616	G=0.639	T=0.361
The Genome Aggregation Database	Europe	Sub	18468	G=0.796	T=0.203
The Genome Aggregation Database	Global	Study-wide	29944	G=0.820	T=0.179
The Genome Aggregation Database	Other	Sub	302	G=0.810	T=0.190
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.848	T=0.151
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.780	T=0.220

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res

P-Value

SNP ID	p-value	Traits	Study
rs16854429	7.29E-05	alcohol dependence	21703634

eQTL of rs16854429 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs16854429 in Fetal Brain

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	72939712	72939862	E081	3887
chr1	72941087	72941542	E081	5262
chr1	72941608	72941689	E081	5783
chr1	72941782	72941896	E081	5957
chr1	72941087	72941542	E082	5262
chr1	72941608	72941689	E082	5783
chr1	72941782	72941896	E082	5957

rs16854429

Genomic Coordinates

Gene: TDRD5, tudor domain containing 5(plus strand)

Population Frequency

P-Value

eQTL of rs16854429 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs16854429 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)