SNP Detail Info-rs989001

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

FBXL17 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0436 (13058/29902,GnomAD)
A=0385 (11214/29118,TOPMED)
A=0362 (1812/5008,1000G)
A=0474 (1827/3854,ALSPAC)
A=0488 (1811/3708,TWINSUK)

Position: chr5:108340620 (GRCh38.p7) (5q21.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 20 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.108340620G>A
GRCh37.p13 chr 5	NC_000005.9:g.107676321G>A

Molecule type	Change	Amino acid[Codon]	SO Term
FBXL17 transcript	NM_001163315.2:c.	N/A	Intron Variant
FBXL17 transcript variant X1	XM_005272048.4:c.	N/A	Intron Variant
FBXL17 transcript variant X11	XM_005272050.4:c.	N/A	Intron Variant
FBXL17 transcript variant X2	XM_011543574.2:c.	N/A	Intron Variant
FBXL17 transcript variant X3	XM_011543575.2:c.	N/A	Intron Variant
FBXL17 transcript variant X4	XM_011543576.2:c.	N/A	Intron Variant
FBXL17 transcript variant X5	XM_011543577.2:c.	N/A	Intron Variant
FBXL17 transcript variant X6	XM_011543578.2:c.	N/A	Intron Variant
FBXL17 transcript variant X7	XM_017009729.1:c.	N/A	Intron Variant
FBXL17 transcript variant X8	XM_011543579.2:c.	N/A	3 Prime UTR Variant
FBXL17 transcript variant X9	XM_011543580.2:c.	N/A	3 Prime UTR Variant
FBXL17 transcript variant X10	XR_427717.3:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.795	A=0.205
1000Genomes	American	Sub	694	G=0.580	A=0.420
1000Genomes	East Asian	Sub	1008	G=0.642	A=0.358
1000Genomes	Europe	Sub	1006	G=0.535	A=0.465
1000Genomes	Global	Study-wide	5008	G=0.638	A=0.362
1000Genomes	South Asian	Sub	978	G=0.570	A=0.430
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.526	A=0.474
The Genome Aggregation Database	African	Sub	8702	G=0.730	A=0.270
The Genome Aggregation Database	American	Sub	832	G=0.590	A=0.410
The Genome Aggregation Database	East Asian	Sub	1610	G=0.652	A=0.348
The Genome Aggregation Database	Europe	Sub	18458	G=0.475	A=0.524
The Genome Aggregation Database	Global	Study-wide	29902	G=0.563	A=0.436
The Genome Aggregation Database	Other	Sub	300	G=0.560	A=0.440
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.614	A=0.385
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.512	A=0.488

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
rs989001	0.000581	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 )
chr5	107714188	107714767	E067	37867
chr5	107715040	107715152	E067	38719
chr5	107715191	107715326	E067	38870
chr5	107647456	107647601	E068	-28720
chr5	107656013	107656181	E068	-20140
chr5	107697379	107697754	E068	21058
chr5	107714188	107714767	E068	37867
chr5	107647456	107647601	E069	-28720
chr5	107697379	107697754	E069	21058
chr5	107715040	107715152	E070	38719
chr5	107715191	107715326	E070	38870
chr5	107714188	107714767	E071	37867
chr5	107715040	107715152	E071	38719
chr5	107715191	107715326	E071	38870
chr5	107647456	107647601	E072	-28720
chr5	107714188	107714767	E072	37867
chr5	107714188	107714767	E073	37867
chr5	107714188	107714767	E074	37867
chr5	107715040	107715152	E074	38719
chr5	107715191	107715326	E074	38870

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr5	107715591	107719044	E067	39270
chr5	107715591	107719044	E068	39270
chr5	107715591	107719044	E069	39270
chr5	107715591	107719044	E070	39270
chr5	107715591	107719044	E071	39270
chr5	107715591	107719044	E072	39270
chr5	107715591	107719044	E073	39270
chr5	107715591	107719044	E074	39270
chr5	107715591	107719044	E081	39270
chr5	107715591	107719044	E082	39270

rs989001