SNP Detail Info-rs139724

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SGSM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0169 (5047/29776,GnomAD)
G=0186 (5438/29116,TOPMED)
G=0137 (685/5008,1000G)
G=0179 (691/3854,ALSPAC)
G=0186 (690/3708,TWINSUK)

Position: chr22:24888862 (GRCh38.p7) (22q11.23)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 6 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 22	NC_000022.11:g.24888862A>G
GRCh37.p13 chr 22	NC_000022.10:g.25284829A>G

Molecule type	Change	Amino acid[Codon]	SO Term
SGSM1 transcript variant 1	NM_001039948.3:c.	N/A	Intron Variant
SGSM1 transcript variant 3	NM_001098497.2:c.	N/A	Intron Variant
SGSM1 transcript variant 4	NM_001098498.2:c.	N/A	Intron Variant
SGSM1 transcript variant 2	NM_133454.3:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.811	G=0.189
1000Genomes	American	Sub	694	A=0.880	G=0.120
1000Genomes	East Asian	Sub	1008	A=0.928	G=0.072
1000Genomes	Europe	Sub	1006	A=0.829	G=0.171
1000Genomes	Global	Study-wide	5008	A=0.863	G=0.137
1000Genomes	South Asian	Sub	978	A=0.890	G=0.110
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.821	G=0.179
The Genome Aggregation Database	African	Sub	8670	A=0.813	G=0.187
The Genome Aggregation Database	American	Sub	826	A=0.890	G=0.110
The Genome Aggregation Database	East Asian	Sub	1616	A=0.928	G=0.072
The Genome Aggregation Database	Europe	Sub	18366	A=0.828	G=0.171
The Genome Aggregation Database	Global	Study-wide	29776	A=0.830	G=0.169
The Genome Aggregation Database	Other	Sub	298	A=0.780	G=0.220
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.813	G=0.186
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.814	G=0.186

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
rs139724	0.000562	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 )
chr22	25290204	25291328	E068	5375
chr22	25291378	25291454	E068	6549
chr22	25327816	25327942	E069	42987
chr22	25327713	25327768	E071	42884
chr22	25327816	25327942	E071	42987
chr22	25327713	25327768	E072	42884

rs139724