SNP Detail Info-rs17644588

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC105374754 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0100 (3018/29944,GnomAD)
A=0059 (1740/29116,TOPMED)
A=0061 (307/5008,1000G)
A=0125 (480/3854,ALSPAC)
A=0131 (485/3708,TWINSUK)

Position: chr2:59353191 (GRCh38.p7) (2p16.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 3 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.59353191G>A
GRCh37.p13 chr 2	NC_000002.11:g.59580326G>A

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105374754 transcript variant X8	XR_001739487.1:n.	N/A	Intron Variant
LOC105374754 transcript variant X2	XR_940126.2:n.	N/A	Intron Variant
LOC105374754 transcript variant X1	XR_940127.2:n.	N/A	Intron Variant
LOC105374754 transcript variant X3	XR_940128.2:n.	N/A	Intron Variant
LOC105374754 transcript variant X4	XR_940129.2:n.	N/A	Intron Variant
LOC105374754 transcript variant X5	XR_940130.2:n.	N/A	Intron Variant
LOC105374754 transcript variant X7	XR_940131.2:n.	N/A	Intron Variant
LOC105374754 transcript variant X7	XR_940132.2:n.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.994	A=0.006
1000Genomes	American	Sub	694	G=0.910	A=0.090
1000Genomes	East Asian	Sub	1008	G=0.930	A=0.070
1000Genomes	Europe	Sub	1006	G=0.891	A=0.109
1000Genomes	Global	Study-wide	5008	G=0.939	A=0.061
1000Genomes	South Asian	Sub	978	G=0.940	A=0.060
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.875	A=0.125
The Genome Aggregation Database	African	Sub	8722	G=0.978	A=0.022
The Genome Aggregation Database	American	Sub	834	G=0.920	A=0.080
The Genome Aggregation Database	East Asian	Sub	1602	G=0.933	A=0.067
The Genome Aggregation Database	Europe	Sub	18484	G=0.856	A=0.143
The Genome Aggregation Database	Global	Study-wide	29944	G=0.899	A=0.100
The Genome Aggregation Database	Other	Sub	302	G=0.970	A=0.030
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.940	A=0.059
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.869	A=0.131

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet

SNP ID	p-value	Traits	Study
rs17644588	0.000728	nicotine dependence	17158188

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 )
chr2	59540266	59540512	E081	-39814
chr2	59540720	59541934	E081	-38392
chr2	59540266	59540512	E082	-39814

rs17644588