SNP Detail Info-rs2817475

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

SMYD3 : Intron Variant
LOC105373270 : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0216 (6477/29910,GnomAD)
T=0261 (7615/29116,TOPMED)
T=0186 (929/5008,1000G)
T=0147 (568/3854,ALSPAC)
T=0139 (515/3708,TWINSUK)

Position: chr1:245798900 (GRCh38.p7) (1q44)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 31 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.245798900C>T
GRCh37.p13 chr 1	NC_000001.10:g.245962202C>T

Molecule type	Change	Amino acid[Codon]	SO Term
SMYD3 transcript variant 1	NM_001167740.1:c.	N/A	Intron Variant
SMYD3 transcript variant 2	NM_022743.2:c.	N/A	Intron Variant
SMYD3 transcript variant X1	XM_011544253.1:c.	N/A	Intron Variant
SMYD3 transcript variant X4	XM_011544254.2:c.	N/A	Intron Variant
SMYD3 transcript variant X5	XM_011544257.1:c.	N/A	Intron Variant
SMYD3 transcript variant X7	XM_011544258.2:c.	N/A	Intron Variant
SMYD3 transcript variant X6	XM_011544259.2:c.	N/A	Intron Variant
SMYD3 transcript variant X6	XM_011544260.1:c.	N/A	Intron Variant
SMYD3 transcript variant X5	XM_011544261.2:c.	N/A	Intron Variant
SMYD3 transcript variant X8	XM_017002094.1:c.	N/A	Intron Variant
SMYD3 transcript variant X9	XM_017002095.1:c.	N/A	Intron Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373270 transcript variant X3	XR_001737771.1:n.	N/A	Upstream Transcript Variant
LOC105373270 transcript variant X1	XR_001737770.1:n.	N/A	N/A
LOC105373270 transcript variant X2	XR_949357.2:n.	N/A	N/A

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.541	T=0.459
1000Genomes	American	Sub	694	C=0.890	T=0.110
1000Genomes	East Asian	Sub	1008	C=0.998	T=0.002
1000Genomes	Europe	Sub	1006	C=0.859	T=0.141
1000Genomes	Global	Study-wide	5008	C=0.814	T=0.186
1000Genomes	South Asian	Sub	978	C=0.890	T=0.110
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.853	T=0.147
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.738	T=0.261
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.861	T=0.139

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

SNP ID	p-value	Traits	Study
rs2817475	0.000467	nicotine smoking	19268276

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 )
chr1	245934933	245935818	E068	-26384
chr1	245927132	245927426	E081	-34776
chr1	245927448	245927596	E081	-34606
chr1	245931960	245932014	E081	-30188
chr1	245934933	245935818	E081	-26384
chr1	245936637	245937171	E081	-25031
chr1	245937453	245937786	E081	-24416
chr1	245961649	245961859	E081	-343
chr1	245972782	245972962	E081	10580
chr1	245973253	245973303	E081	11051
chr1	245973620	245973670	E081	11418
chr1	245973680	245974264	E081	11478
chr1	245974316	245974559	E081	12114
chr1	245974621	245974756	E081	12419
chr1	245974815	245974957	E081	12613
chr1	245975362	245975500	E081	13160
chr1	245986188	245987044	E081	23986
chr1	245998754	245999314	E081	36552
chr1	245999491	245999629	E081	37289
chr1	245927132	245927426	E082	-34776
chr1	245927448	245927596	E082	-34606
chr1	245972782	245972962	E082	10580
chr1	245973253	245973303	E082	11051
chr1	245973620	245973670	E082	11418
chr1	245973680	245974264	E082	11478
chr1	245974621	245974756	E082	12419
chr1	245974815	245974957	E082	12613
chr1	245975362	245975500	E082	13160
chr1	245996803	245996865	E082	34601
chr1	245997397	245997502	E082	35195
chr1	245998754	245999314	E082	36552

rs2817475