rs3743445

Homo sapiens
C>T
VPS33B : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0170 (5109/29974,GnomAD)
T=0157 (4594/29118,TOPMED)
T=0261 (1308/5008,1000G)
T=0119 (458/3854,ALSPAC)
T=0111 (412/3708,TWINSUK)
chr15:91017952 (GRCh38.p7) (15q26.1)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.91017952C>T
GRCh37.p13 chr 15NC_000015.9:g.91561182C>T
VPS33B RefSeqGene LRG_884

Gene: VPS33B, VPS33B, late endosome and lysosome associated(minus strand)

Molecule type Change Amino acid[Codon] SO Term
VPS33B transcript variant 2NM_001289148.1:c.N/AIntron Variant
VPS33B transcript variant 3NM_001289149.1:c.N/AIntron Variant
VPS33B transcript variant 1NM_018668.4:c.N/AIntron Variant
VPS33B transcript variant X2XM_005254887.1:c.N/AIntron Variant
VPS33B transcript variant X1XM_011521448.1:c.N/AIntron Variant
VPS33B transcript variant X4XM_017022075.1:c.N/AIntron Variant
VPS33B transcript variant X5XM_017022076.1:c.N/AIntron Variant
VPS33B transcript variant X3XM_011521449.2:c.N/AGenic Upstream Transcript Variant
VPS33B transcript variant X6XR_001751213.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.820T=0.180
1000GenomesAmericanSub694C=0.750T=0.250
1000GenomesEast AsianSub1008C=0.462T=0.538
1000GenomesEuropeSub1006C=0.869T=0.131
1000GenomesGlobalStudy-wide5008C=0.739T=0.261
1000GenomesSouth AsianSub978C=0.780T=0.220
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.881T=0.119
The Genome Aggregation DatabaseAfricanSub8722C=0.820T=0.180
The Genome Aggregation DatabaseAmericanSub836C=0.720T=0.280
The Genome Aggregation DatabaseEast AsianSub1618C=0.470T=0.530
The Genome Aggregation DatabaseEuropeSub18496C=0.870T=0.130
The Genome Aggregation DatabaseGlobalStudy-wide29974C=0.829T=0.170
The Genome Aggregation DatabaseOtherSub302C=0.870T=0.130
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.842T=0.157
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.889T=0.111
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
rs37434450.00036alcohol dependence20201924

eQTL of rs3743445 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:91561182MAN2A2ENSG00000196547.10C>T1.7425e-18115734Cerebellum
Chr15:91561182RCCD1ENSG00000166965.8C>T1.6411e-1662156Cerebellum
Chr15:91561182PRC1-AS1ENSG00000258725.1C>T2.3706e-845092Cerebellum
Chr15:91561182RCCD1ENSG00000166965.8C>T1.3466e-1462156Frontal_Cortex_BA9
Chr15:91561182RCCD1ENSG00000166965.8C>T4.4186e-1362156Cortex
Chr15:91561182RCCD1ENSG00000166965.8C>T4.8876e-1862156Cerebellar_Hemisphere
Chr15:91561182PRC1-AS1ENSG00000258725.1C>T1.4168e-545092Cerebellar_Hemisphere
Chr15:91561182RCCD1ENSG00000166965.8C>T3.4773e-1462156Caudate_basal_ganglia
Chr15:91561182RCCD1ENSG00000166965.8C>T3.8776e-962156Anterior_cingulate_cortex
Chr15:91561182RCCD1ENSG00000166965.8C>T3.7564e-1662156Nucleus_accumbens_basal_ganglia

meQTL of rs3743445 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 )
chr159156124391561315E06761
chr159156148791561541E067305
chr159156437691564486E0683194
chr159159277891593536E06831596
chr159156091491561212E0690
chr159156124391561315E06961
chr159153152291532011E070-29171
chr159153201491532165E070-29017
chr159153489291535160E070-26022
chr159153518591535307E070-25875
chr159153532191535405E070-25777
chr159153550691535616E070-25566
chr159156148791561541E070305
chr159156156691561646E070384
chr159156169191561763E070509
chr159156373791563860E0702555
chr159156427091564320E0703088
chr159156437691564486E0703194
chr159156091491561212E0710
chr159156124391561315E07161
chr159156148791561541E071305
chr159156156691561646E071384
chr159156169191561763E071509
chr159156124391561315E07261
chr159156148791561541E072305
chr159156156691561646E072384
chr159156169191561763E072509
chr159156183091561884E072648
chr159156189591561935E072713
chr159156373791563860E0722555
chr159156427091564320E0723088
chr159156437691564486E0723194
chr159159890891599032E07237726
chr159160717191607211E07245989
chr159156373791563860E0742555
chr159156427091564320E0743088
chr159156437691564486E0743194
chr159156427091564320E0813088
chr159156437691564486E0813194
chr159156275391562809E0821571
chr159156427091564320E0823088









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr159153634891539047E067-22135
chr159156479591566467E0673613
chr159159909591599563E06737913
chr159159957091599655E06738388
chr159153634891539047E068-22135
chr159156479591566467E0683613
chr159159909591599563E06837913
chr159159957091599655E06838388
chr159153634891539047E069-22135
chr159156479591566467E0693613
chr159159909591599563E06937913
chr159159957091599655E06938388
chr159153587391536278E070-24904
chr159153634891539047E070-22135
chr159153907291539143E070-22039
chr159156479591566467E0703613
chr159153634891539047E071-22135
chr159156479591566467E0713613
chr159159909591599563E07137913
chr159159957091599655E07138388
chr159153634891539047E072-22135
chr159156479591566467E0723613
chr159159909591599563E07237913
chr159159957091599655E07238388
chr159153634891539047E073-22135
chr159156479591566467E0733613
chr159159909591599563E07337913
chr159159957091599655E07338388
chr159153634891539047E074-22135
chr159156479591566467E0743613
chr159159909591599563E07437913
chr159153634891539047E081-22135
chr159156479591566467E0813613
chr159153587391536278E082-24904
chr159153634891539047E082-22135
chr159156479591566467E0823613