SNP Detail Info-rs9289666

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SLC9A9 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0139 (4191/29972,GnomAD)
A==0152 (4426/29118,TOPMED)
A==0140 (703/5008,1000G)
A==0117 (451/3854,ALSPAC)
A==0117 (432/3708,TWINSUK)

Position: chr3:143526140 (GRCh38.p7) (3q24)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 24 Enhancers around

Promoter: 0 Promoter around

Molecule type	Change	Amino acid[Codon]	SO Term
SLC9A9 transcript	NM_173653.3:c.	N/A	Intron Variant
SLC9A9 transcript variant X3	XM_011512703.2:c.	N/A	Intron Variant
SLC9A9 transcript variant X1	XM_017006202.1:c.	N/A	Intron Variant
SLC9A9 transcript variant X2	XM_017006203.1:c.	N/A	Intron Variant
SLC9A9 transcript variant X4	XM_011512704.2:c.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.248	G=0.752
1000Genomes	American	Sub	694	A=0.090	G=0.910
1000Genomes	East Asian	Sub	1008	A=0.021	G=0.979
1000Genomes	Europe	Sub	1006	A=0.093	G=0.907
1000Genomes	Global	Study-wide	5008	A=0.140	G=0.860
1000Genomes	South Asian	Sub	978	A=0.200	G=0.800
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.117	G=0.883
The Genome Aggregation Database	African	Sub	8722	A=0.209	G=0.791
The Genome Aggregation Database	American	Sub	838	A=0.090	G=0.910
The Genome Aggregation Database	East Asian	Sub	1614	A=0.007	G=0.993
The Genome Aggregation Database	Europe	Sub	18496	A=0.121	G=0.878
The Genome Aggregation Database	Global	Study-wide	29972	A=0.139	G=0.860
The Genome Aggregation Database	Other	Sub	302	A=0.100	G=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.152	G=0.848
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.117	G=0.883

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
rs9289666	0.0003	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 )
chr3	143220226	143220980	E067	-24002
chr3	143286555	143286690	E067	41573
chr3	143271742	143272097	E068	26760
chr3	143272183	143272245	E068	27201
chr3	143284776	143285190	E068	39794
chr3	143220226	143220980	E069	-24002
chr3	143226677	143226849	E069	-18133
chr3	143226971	143227360	E069	-17622
chr3	143255678	143255877	E069	10696
chr3	143220226	143220980	E070	-24002
chr3	143286417	143286484	E070	41435
chr3	143286555	143286690	E070	41573
chr3	143286818	143286967	E070	41836
chr3	143220226	143220980	E071	-24002
chr3	143221014	143221175	E071	-23807
chr3	143226677	143226849	E071	-18133
chr3	143255678	143255877	E071	10696
chr3	143255948	143256338	E071	10966
chr3	143220226	143220980	E072	-24002
chr3	143220226	143220980	E074	-24002
chr3	143255678	143255877	E074	10696
chr3	143255948	143256338	E074	10966
chr3	143272183	143272245	E074	27201
chr3	143268452	143268566	E081	23470

rs9289666