rs1549738

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0232 (6952/29948,GnomAD)
G==0262 (7635/29118,TOPMED)
G==0309 (1545/5008,1000G)
G==0123 (475/3854,ALSPAC)
G==0118 (437/3708,TWINSUK)

Position: chr2:217253999 (GRCh38.p7) (2q35)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 47 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.217253999G>A
GRCh37.p13 chr 2	NC_000002.11:g.218118722G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.457	A=0.543
1000Genomes	American	Sub	694	G=0.160	A=0.840
1000Genomes	East Asian	Sub	1008	G=0.390	A=0.610
1000Genomes	Europe	Sub	1006	G=0.134	A=0.866
1000Genomes	Global	Study-wide	5008	G=0.309	A=0.691
1000Genomes	South Asian	Sub	978	G=0.310	A=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.123	A=0.877
The Genome Aggregation Database	African	Sub	8712	G=0.413	A=0.587
The Genome Aggregation Database	American	Sub	838	G=0.190	A=0.810
The Genome Aggregation Database	East Asian	Sub	1612	G=0.428	A=0.572
The Genome Aggregation Database	Europe	Sub	18484	G=0.131	A=0.869
The Genome Aggregation Database	Global	Study-wide	29948	G=0.232	A=0.767
The Genome Aggregation Database	Other	Sub	302	G=0.290	A=0.710
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.262	A=0.737
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.118	A=0.882

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
rs1549738	4.88E-05	nicotine smoking	19268276

eQTL of rs1549738 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 rs1549738 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 )
chr2	218113770	218113851	E067	-4871
chr2	218113866	218114019	E067	-4703
chr2	218143622	218143688	E067	24900
chr2	218112689	218113744	E068	-4978
chr2	218113770	218113851	E068	-4871
chr2	218113866	218114019	E068	-4703
chr2	218140007	218140057	E068	21285
chr2	218142324	218142963	E068	23602
chr2	218143622	218143688	E068	24900
chr2	218143831	218144788	E068	25109
chr2	218112689	218113744	E069	-4978
chr2	218113770	218113851	E069	-4871
chr2	218113866	218114019	E069	-4703
chr2	218143622	218143688	E069	24900
chr2	218143831	218144788	E069	25109
chr2	218112689	218113744	E070	-4978
chr2	218113770	218113851	E070	-4871
chr2	218113866	218114019	E070	-4703
chr2	218085955	218086242	E071	-32480
chr2	218112689	218113744	E071	-4978
chr2	218113770	218113851	E071	-4871
chr2	218113866	218114019	E071	-4703
chr2	218142324	218142963	E071	23602
chr2	218143622	218143688	E071	24900
chr2	218143831	218144788	E071	25109
chr2	218112689	218113744	E072	-4978
chr2	218113770	218113851	E072	-4871
chr2	218113866	218114019	E072	-4703
chr2	218142324	218142963	E072	23602
chr2	218143622	218143688	E072	24900
chr2	218143831	218144788	E072	25109
chr2	218112689	218113744	E073	-4978
chr2	218113770	218113851	E073	-4871
chr2	218113866	218114019	E073	-4703
chr2	218112208	218112675	E074	-6047
chr2	218113770	218113851	E074	-4871
chr2	218113866	218114019	E074	-4703
chr2	218142324	218142963	E074	23602
chr2	218143622	218143688	E074	24900
chr2	218143831	218144788	E074	25109
chr2	218166424	218166503	E074	47702
chr2	218112208	218112675	E081	-6047
chr2	218112689	218113744	E081	-4978
chr2	218112208	218112675	E082	-6047
chr2	218112689	218113744	E082	-4978
chr2	218113770	218113851	E082	-4871
chr2	218113866	218114019	E082	-4703