rs778139

Homo sapiens
G>A
USP34 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0468 (14021/29912,GnomAD)
A=0468 (13650/29116,TOPMED)
A=0379 (1900/5008,1000G)
A=0484 (1867/3854,ALSPAC)
A=0484 (1794/3708,TWINSUK)
chr2:61457429 (GRCh38.p7) (2p15)
AD
GWASdb2
1   publication(s)
See rs on genome
122 Enhancers around
19 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.61457429G>A
GRCh37.p13 chr 2NC_000002.11:g.61684564G>A

Gene: USP34, ubiquitin specific peptidase 34(minus strand)

Molecule type Change Amino acid[Codon] SO Term
USP34 transcriptNM_014709.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.579A=0.421
1000GenomesAmericanSub694G=0.570A=0.430
1000GenomesEast AsianSub1008G=0.702A=0.298
1000GenomesEuropeSub1006G=0.496A=0.504
1000GenomesGlobalStudy-wide5008G=0.621A=0.379
1000GenomesSouth AsianSub978G=0.750A=0.250
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.516A=0.484
The Genome Aggregation DatabaseAfricanSub8686G=0.547A=0.453
The Genome Aggregation DatabaseAmericanSub836G=0.630A=0.370
The Genome Aggregation DatabaseEast AsianSub1612G=0.748A=0.252
The Genome Aggregation DatabaseEuropeSub18476G=0.500A=0.499
The Genome Aggregation DatabaseGlobalStudy-wide29912G=0.531A=0.468
The Genome Aggregation DatabaseOtherSub302G=0.490A=0.510
Trans-Omics for Precision MedicineGlobalStudy-wide29116G=0.531A=0.468
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.516A=0.484
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs7781390.000991alcohol consumption (maxi-drinks)24277619

eQTL of rs778139 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:61684564KIAA1841ENSG00000162929.9G>A1.6156e-3391558Cerebellum
Chr2:61684564RP11-493E12.1ENSG00000271889.1G>A2.2345e-5295324Cerebellum
Chr2:61684564AHSA2ENSG00000173209.18G>A0.0000e+0280011Cerebellum
Chr2:61684564AHSA2ENSG00000173209.18G>A4.8179e-18280011Frontal_Cortex_BA9
Chr2:61684564AHSA2ENSG00000173209.18G>A1.5965e-11280011Hypothalamus
Chr2:61684564AHSA2ENSG00000173209.18G>A8.2400e-24280011Cortex
Chr2:61684564AHSA2ENSG00000173209.18G>A5.6344e-20280011Cerebellar_Hemisphere
Chr2:61684564RP11-493E12.2ENSG00000273302.1G>A3.0236e-5257450Cerebellar_Hemisphere
Chr2:61684564KIAA1841ENSG00000162929.9G>A5.0439e-5391558Caudate_basal_ganglia
Chr2:61684564AHSA2ENSG00000173209.18G>A2.9793e-18280011Caudate_basal_ganglia
Chr2:61684564AHSA2ENSG00000173209.18G>A1.2695e-13280011Brain_Spinal_cord_cervical
Chr2:61684564RP11-493E12.2ENSG00000273302.1G>A4.1019e-6257450Brain_Spinal_cord_cervical
Chr2:61684564AHSA2ENSG00000173209.18G>A2.0917e-14280011Hippocampus
Chr2:61684564KIAA1841ENSG00000162929.9G>A2.0653e-4391558Putamen_basal_ganglia
Chr2:61684564AHSA2ENSG00000173209.18G>A7.8889e-18280011Putamen_basal_ganglia
Chr2:61684564AHSA2ENSG00000173209.18G>A1.7158e-16280011Anterior_cingulate_cortex
Chr2:61684564AHSA2ENSG00000173209.18G>A7.0058e-21280011Nucleus_accumbens_basal_ganglia
Chr2:61684564AHSA2ENSG00000173209.18G>A1.3352e-10280011Amygdala

meQTL of rs778139 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 )
chr26164831761648345E067-36219
chr26164842361648534E067-36030
chr26164874161648861E067-35703
chr26164889561649009E067-35555
chr26164907861649128E067-35436
chr26165247161652696E067-31868
chr26165274161652951E067-31613
chr26165315661654028E067-30536
chr26166085461661044E067-23520
chr26166109861661237E067-23327
chr26166684961666895E067-17669
chr26166712261667172E067-17392
chr26167053561670645E067-13919
chr26168334661683463E067-1101
chr26168349561683599E067-965
chr26168722061687669E0672656
chr26163740261637548E068-47016
chr26163756061637635E068-46929
chr26165096761651104E068-33460
chr26165315661654028E068-30536
chr26166684961666895E068-17669
chr26166712261667172E068-17392
chr26166914961669261E068-15303
chr26168487561684933E068311
chr26168508761685137E068523
chr26169103661691204E0686472
chr26169126761691382E0686703
chr26169145561691934E0686891
chr26170535761705602E06820793
chr26170586461705972E06821300
chr26173447761734527E06849913
chr26164813361648198E069-36366
chr26164831761648345E069-36219
chr26164842361648534E069-36030
chr26164874161648861E069-35703
chr26164889561649009E069-35555
chr26164907861649128E069-35436
chr26164921561649267E069-35297
chr26165247161652696E069-31868
chr26165274161652951E069-31613
chr26165315661654028E069-30536
chr26166642861666542E069-18022
chr26166684961666895E069-17669
chr26166712261667172E069-17392
chr26166749961667568E069-16996
chr26168591161685961E0691347
chr26168722061687669E0692656
chr26169980561699904E06915241
chr26169990961700028E06915345
chr26170535761705602E06920793
chr26168334661683463E070-1101
chr26168349561683599E070-965
chr26164831761648345E071-36219
chr26164842361648534E071-36030
chr26164874161648861E071-35703
chr26164982161649864E071-34700
chr26165274161652951E071-31613
chr26165315661654028E071-30536
chr26166333561663565E071-20999
chr26166359561663778E071-20786
chr26166642861666542E071-18022
chr26166684961666895E071-17669
chr26166712261667172E071-17392
chr26166749961667568E071-16996
chr26168722061687669E0712656
chr26170453661704673E07119972
chr26170535761705602E07120793
chr26170586461705972E07121300
chr26170601761706113E07121453
chr26164831761648345E072-36219
chr26164842361648534E072-36030
chr26164874161648861E072-35703
chr26164889561649009E072-35555
chr26165096761651104E072-33460
chr26165218761652422E072-32142
chr26165247161652696E072-31868
chr26165274161652951E072-31613
chr26165315661654028E072-30536
chr26166085461661044E072-23520
chr26166109861661237E072-23327
chr26166684961666895E072-17669
chr26166712261667172E072-17392
chr26166749961667568E072-16996
chr26166956261669675E072-14889
chr26166970861669883E072-14681
chr26166990961669963E072-14601
chr26168334661683463E072-1101
chr26168349561683599E072-965
chr26168455661684620E0720
chr26168487561684933E072311
chr26168508761685137E072523
chr26169521561695265E07210651
chr26170535761705602E07220793
chr26165247161652696E073-31868
chr26165274161652951E073-31613
chr26165315661654028E073-30536
chr26166085461661044E073-23520
chr26166109861661237E073-23327
chr26166147161661834E073-22730
chr26166684961666895E073-17669
chr26166712261667172E073-17392
chr26166867261668930E073-15634
chr26166902161669105E073-15459
chr26166914961669261E073-15303
chr26166941861669505E073-15059
chr26166956261669675E073-14889
chr26166970861669883E073-14681
chr26166990961669963E073-14601
chr26168591161685961E0731347
chr26165274161652951E074-31613
chr26165315661654028E074-30536
chr26166684961666895E074-17669
chr26166712261667172E074-17392
chr26166749961667568E074-16996
chr26166867261668930E074-15634
chr26168722061687669E0742656
chr26173447761734527E07449913
chr26169980561699904E08115241
chr26169990961700028E08115345
chr26169521561695265E08210651
chr26169980561699904E08215241
chr26169990961700028E08215345










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr26169660261696799E06712038
chr26169684161699541E06712277
chr26169660261696799E06812038
chr26169684161699541E06812277
chr26169684161699541E06912277
chr26169660261696799E07012038
chr26169684161699541E07012277
chr26169660261696799E07112038
chr26169684161699541E07112277
chr26169660261696799E07212038
chr26169684161699541E07212277
chr26169660261696799E07312038
chr26169684161699541E07312277
chr26169660261696799E07412038
chr26169684161699541E07412277
chr26169660261696799E08112038
chr26169684161699541E08112277
chr26169660261696799E08212038
chr26169684161699541E08212277