SNP Detail Info-rs2303904

Organism: Homo sapiens

Alleles: A>C / A>G

Gene : Feature

SMYD5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0435 (12993/29862,GnomAD)
G=0450 (13118/29116,TOPMED)
A==0441 (5738/13006,GO-ESP)
G=0425 (2128/5008,1000G)
G=0409 (1575/3854,ALSPAC)
G=0431 (1598/3708,TWINSUK)

Position: chr2:73220647 (GRCh38.p7) (2p13.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer 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.73220647A>C
GRCh38.p7 chr 2	NC_000002.12:g.73220647A>G
GRCh37.p13 chr 2	NC_000002.11:g.73447775A>C
GRCh37.p13 chr 2	NC_000002.11:g.73447775A>G

Gene: SMYD5, SMYD family member 5(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SMYD5 transcript	NM_006062.2:c.	N/A	Intron Variant
SMYD5 transcript variant X2	XM_006711918.3:c.	N/A	Intron Variant
SMYD5 transcript variant X1	XM_017003163.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.449	G=0.551
1000Genomes	American	Sub	694	A=0.620	G=0.380
1000Genomes	East Asian	Sub	1008	A=0.608	G=0.392
1000Genomes	Europe	Sub	1006	A=0.583	G=0.417
1000Genomes	Global	Study-wide	5008	A=0.575	G=0.425
1000Genomes	South Asian	Sub	978	A=0.670	G=0.330
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.591	G=0.409
The Genome Aggregation Database	African	Sub	8680	A=0.468	G=0.532
The Genome Aggregation Database	American	Sub	836	A=0.660	G=0.340
The Genome Aggregation Database	East Asian	Sub	1614	A=0.618	G=0.382
The Genome Aggregation Database	Europe	Sub	18430	A=0.601	G=0.399
The Genome Aggregation Database	Global	Study-wide	29862	A=0.564	G=0.435
The Genome Aggregation Database	Other	Sub	302	A=0.610	G=0.390
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.549	G=0.450
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.569	G=0.431

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
rs2303904	0.000768	nicotine smoking	19268276

eQTL of rs2303904 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:73447775	NOTO	ENSG00000214513.3	A>G	1.8643e-11	18389	Cerebellar_Hemisphere

meQTL of rs2303904 in Fetal Brain

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

rs2303904