rs2809985

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PLD5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0407 (12182/29934,GnomAD)
G=0459 (13377/29116,TOPMED)
G=0428 (2145/5008,1000G)
G=0380 (1466/3854,ALSPAC)
G=0384 (1424/3708,TWINSUK)

Position: chr1:242399419 (GRCh38.p7) (1q43)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 14 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.242399419A>G
GRCh37.p13 chr 1	NC_000001.10:g.242562721A>G

Gene: PLD5, phospholipase D family member 5(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PLD5 transcript variant 2	NM_001195811.1:c.	N/A	Intron Variant
PLD5 transcript variant 3	NM_001195812.1:c.	N/A	Intron Variant
PLD5 transcript variant 4	NM_001320272.1:c.	N/A	Intron Variant
PLD5 transcript variant 1	NM_152666.2:c.	N/A	Intron Variant
PLD5 transcript variant X1	XM_006711752.2:c.	N/A	Intron Variant
PLD5 transcript variant X3	XM_011544115.2:c.	N/A	Intron Variant
PLD5 transcript variant X4	XM_011544116.2:c.	N/A	Intron Variant
PLD5 transcript variant X8	XM_011544120.2:c.	N/A	Intron Variant
PLD5 transcript variant X4	XM_017000567.1:c.	N/A	Intron Variant
PLD5 transcript variant X5	XM_017000568.1:c.	N/A	Intron Variant
PLD5 transcript variant X9	XM_017000569.1:c.	N/A	Intron Variant
PLD5 transcript variant X7	XM_011544119.2:c.	N/A	Genic Upstream Transcript Variant
PLD5 transcript variant X12	XM_011544121.2:c.	N/A	Genic Upstream Transcript Variant
PLD5 transcript variant X9	XM_011544122.2:c.	N/A	Genic Upstream Transcript Variant
PLD5 transcript variant X10	XM_017000570.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.437	G=0.563
1000Genomes	American	Sub	694	A=0.610	G=0.390
1000Genomes	East Asian	Sub	1008	A=0.780	G=0.220
1000Genomes	Europe	Sub	1006	A=0.596	G=0.404
1000Genomes	Global	Study-wide	5008	A=0.572	G=0.428
1000Genomes	South Asian	Sub	978	A=0.480	G=0.520
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.620	G=0.380
The Genome Aggregation Database	African	Sub	8714	A=0.466	G=0.534
The Genome Aggregation Database	American	Sub	836	A=0.590	G=0.410
The Genome Aggregation Database	East Asian	Sub	1616	A=0.764	G=0.236
The Genome Aggregation Database	Europe	Sub	18466	A=0.637	G=0.362
The Genome Aggregation Database	Global	Study-wide	29934	A=0.593	G=0.407
The Genome Aggregation Database	Other	Sub	302	A=0.640	G=0.360
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.540	G=0.459
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.616	G=0.384

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs2809985	0.000381	nicotine smoking	19268276

eQTL of rs2809985 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 rs2809985 in Fetal Brain

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

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	242579928	242580262	E068	17207
chr1	242580667	242580760	E068	17946
chr1	242611841	242611930	E068	49120
chr1	242611987	242612101	E068	49266
chr1	242612140	242612255	E068	49419
chr1	242611841	242611930	E069	49120
chr1	242611987	242612101	E069	49266
chr1	242591537	242591611	E070	28816
chr1	242591805	242591951	E070	29084
chr1	242592228	242592562	E070	29507
chr1	242579928	242580262	E074	17207
chr1	242580667	242580760	E074	17946
chr1	242581135	242581195	E074	18414
chr1	242612348	242612430	E081	49627