rs885624

Homo sapiens
T>A / T>C
FBXL17 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0320 (9584/29892,GnomAD)
C=0304 (8877/29118,TOPMED)
C=0338 (1694/5008,1000G)
C=0290 (1117/3854,ALSPAC)
C=0285 (1056/3708,TWINSUK)
chr5:107964954 (GRCh38.p7) (5q21.3)
ND
GWASdb2
2   publication(s)
See rs on genome
10 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.107964954T>A
GRCh38.p7 chr 5NC_000005.10:g.107964954T>C
GRCh37.p13 chr 5NC_000005.9:g.107300655T>A
GRCh37.p13 chr 5NC_000005.9:g.107300655T>C

Gene: FBXL17, F-box and leucine-rich repeat protein 17(minus strand)

Molecule type Change Amino acid[Codon] SO Term
FBXL17 transcriptNM_001163315.2:c.N/AIntron Variant
FBXL17 transcript variant X1XM_005272048.4:c.N/AIntron Variant
FBXL17 transcript variant X2XM_011543574.2:c.N/AIntron Variant
FBXL17 transcript variant X3XM_011543575.2:c.N/AIntron Variant
FBXL17 transcript variant X11XM_005272050.4:c.N/AGenic Downstream Transcript Variant
FBXL17 transcript variant X4XM_011543576.2:c.N/AGenic Downstream Transcript Variant
FBXL17 transcript variant X5XM_011543577.2:c.N/AGenic Downstream Transcript Variant
FBXL17 transcript variant X6XM_011543578.2:c.N/AGenic Downstream Transcript Variant
FBXL17 transcript variant X8XM_011543579.2:c.N/AGenic Downstream Transcript Variant
FBXL17 transcript variant X9XM_011543580.2:c.N/AGenic Downstream Transcript Variant
FBXL17 transcript variant X7XM_017009729.1:c.N/AGenic Downstream Transcript Variant
FBXL17 transcript variant X10XR_427717.3:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.654C=0.346
1000GenomesAmericanSub694T=0.760C=0.240
1000GenomesEast AsianSub1008T=0.603C=0.397
1000GenomesEuropeSub1006T=0.715C=0.285
1000GenomesGlobalStudy-wide5008T=0.662C=0.338
1000GenomesSouth AsianSub978T=0.610C=0.390
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.710C=0.290
The Genome Aggregation DatabaseAfricanSub8712T=0.667C=0.333
The Genome Aggregation DatabaseAmericanSub836T=0.760C=0.240
The Genome Aggregation DatabaseEast AsianSub1594T=0.600C=0.400
The Genome Aggregation DatabaseEuropeSub18448T=0.689C=0.311
The Genome Aggregation DatabaseGlobalStudy-wide29892T=0.679C=0.320
The Genome Aggregation DatabaseOtherSub302T=0.660C=0.340
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.695C=0.304
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.715C=0.285
PMID Title Author Journal
19247474Genome-wide and candidate gene association study of cigarette smoking behaviors.Caporaso NPLoS One
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs8856240.000519nicotine dependence17158188

eQTL of rs885624 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs885624 in Fetal Brain

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

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr58940829389408348E0674371
chr58942741589427490E06923493
chr58940829389408348E0704371
chr58942680889426910E07022886
chr58943062989431123E07126707
chr58943133689431518E07127414
chr58942680889426910E08122886
chr58942741589427490E08123493
chr58942680889426910E08222886
chr58942741589427490E08223493