rs585961

Homo sapiens
G>A
FBXL20 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0368 (10998/29868,GnomAD)
A=0448 (13052/29118,TOPMED)
A=0362 (1815/5008,1000G)
A=0255 (981/3854,ALSPAC)
A=0264 (978/3708,TWINSUK)
chr17:39287783 (GRCh38.p7) (17q12)
AD
GWASdb2
1   publication(s)
See rs on genome
22 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.39287783G>A
GRCh37.p13 chr 17NC_000017.10:g.37444036G>A

Gene: FBXL20, F-box and leucine-rich repeat protein 20(minus strand)

Molecule type Change Amino acid[Codon] SO Term
FBXL20 transcript variant 2NM_001184906.1:c.N/AIntron Variant
FBXL20 transcript variant 1NM_032875.2:c.N/AIntron Variant
FBXL20 transcript variant X2XM_005257746.3:c.N/AIntron Variant
FBXL20 transcript variant X1XM_005257747.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.278A=0.722
1000GenomesAmericanSub694G=0.660A=0.340
1000GenomesEast AsianSub1008G=0.736A=0.264
1000GenomesEuropeSub1006G=0.748A=0.252
1000GenomesGlobalStudy-wide5008G=0.638A=0.362
1000GenomesSouth AsianSub978G=0.890A=0.110
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.745A=0.255
The Genome Aggregation DatabaseAfricanSub8690G=0.336A=0.664
The Genome Aggregation DatabaseAmericanSub838G=0.690A=0.310
The Genome Aggregation DatabaseEast AsianSub1584G=0.697A=0.303
The Genome Aggregation DatabaseEuropeSub18454G=0.762A=0.237
The Genome Aggregation DatabaseGlobalStudy-wide29868G=0.631A=0.368
The Genome Aggregation DatabaseOtherSub302G=0.650A=0.350
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.551A=0.448
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.736A=0.264
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs5859610.000356alcohol dependence20201924

eQTL of rs585961 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 rs585961 in Fetal Brain

Probe ID Position Gene beta p-value
cg07936489chr17:37558343FBXL200.01933712867080671.7063e-14
cg15445000chr17:37608096MED1-0.04612940573617265.1568e-12
cg00129232chr17:37814104STARD30.006097714374915933.4725e-10
cg20243544chr17:37824526PNMT-0.01445859032405279.5907e-10
cg07936489chr17:37558343FBXL200.0193371291.7100e-14

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 )
chr173740023037401826E067-42210
chr173746289037463100E06718854
chr173746316737463309E06719131
chr173739426537395286E068-48750
chr173746227437462402E06818238
chr173746247637462567E06818440
chr173746257937462714E06818543
chr173746276037462810E06818724
chr173746289037463100E06818854
chr173746316737463309E06819131
chr173739426537395286E071-48750
chr173746227437462402E07118238
chr173746247637462567E07118440
chr173746257937462714E07118543
chr173746276037462810E07118724
chr173746289037463100E07118854
chr173746316737463309E07119131
chr173749095337491073E07146917
chr173739426537395286E073-48750
chr173740023037401826E073-42210
chr173746316737463309E07319131
chr173739426537395286E074-48750