rs12667392

Homo sapiens
A>C
USP42 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0086 (2596/29964,GnomAD)
C=0077 (2246/29118,TOPMED)
C=0081 (407/5008,1000G)
C=0046 (179/3854,ALSPAC)
C=0047 (176/3708,TWINSUK)
chr7:6112051 (GRCh38.p7) (7p22.1)
ND
GWASdb2
1   publication(s)
See rs on genome
87 Enhancers around
38 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.6112051A>C
GRCh37.p13 chr 7NC_000007.13:g.6151682A>C

Gene: USP42, ubiquitin specific peptidase 42(plus strand)

Molecule type Change Amino acid[Codon] SO Term
USP42 transcriptNM_032172.2:c.N/AIntron Variant
USP42 transcript variant X7XM_005249883.4:c.N/AIntron Variant
USP42 transcript variant X1XM_006715790.1:c.N/AIntron Variant
USP42 transcript variant X5XM_006715791.2:c.N/AIntron Variant
USP42 transcript variant X4XM_011515573.1:c.N/AIntron Variant
USP42 transcript variant X7XM_011515574.1:c.N/AIntron Variant
USP42 transcript variant X9XM_011515578.1:c.N/AIntron Variant
USP42 transcript variant X8XM_011515577.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.846C=0.154
1000GenomesAmericanSub694A=0.960C=0.040
1000GenomesEast AsianSub1008A=0.971C=0.029
1000GenomesEuropeSub1006A=0.950C=0.050
1000GenomesGlobalStudy-wide5008A=0.919C=0.081
1000GenomesSouth AsianSub978A=0.900C=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.954C=0.046
The Genome Aggregation DatabaseAfricanSub8730A=0.865C=0.135
The Genome Aggregation DatabaseAmericanSub838A=0.960C=0.040
The Genome Aggregation DatabaseEast AsianSub1620A=0.964C=0.036
The Genome Aggregation DatabaseEuropeSub18474A=0.929C=0.070
The Genome Aggregation DatabaseGlobalStudy-wide29964A=0.913C=0.086
The Genome Aggregation DatabaseOtherSub302A=0.960C=0.040
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.922C=0.077
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.953C=0.047
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs126673929.77E-06alcohol and nictotine co-dependence20158304

eQTL of rs12667392 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 rs12667392 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 )
chr761981226198311E06746440
chr761984016198502E06746719
chr761985176198637E06746835
chr761988156199072E06747133
chr761991876199342E06747505
chr761993446199454E06747662
chr761995716200285E06747889
chr761467206146852E068-4830
chr761978416197922E06846159
chr761980076198097E06846325
chr761981226198311E06846440
chr761984016198502E06846719
chr761985176198637E06846835
chr761995716200285E06847889
chr762004276200544E06848745
chr761427506142819E069-8863
chr761430086143116E069-8566
chr761431946143357E069-8325
chr761467206146852E069-4830
chr761469046146948E069-4734
chr761978416197922E06946159
chr761980076198097E06946325
chr761981226198311E06946440
chr761984016198502E06946719
chr761985176198637E06946835
chr761988156199072E06947133
chr761991876199342E06947505
chr761993446199454E06947662
chr761995716200285E06947889
chr761427506142819E070-8863
chr761430086143116E070-8566
chr761431946143357E070-8325
chr761467206146852E070-4830
chr761991876199342E07047505
chr761993446199454E07047662
chr761469046146948E071-4734
chr761975586197622E07145876
chr761976526197695E07145970
chr761978416197922E07146159
chr761980076198097E07146325
chr761981226198311E07146440
chr761984016198502E07146719
chr761985176198637E07146835
chr761988156199072E07147133
chr761991876199342E07147505
chr761993446199454E07147662
chr761995716200285E07147889
chr762004276200544E07148745
chr761978416197922E07246159
chr761980076198097E07246325
chr761981226198311E07246440
chr761984016198502E07246719
chr761985176198637E07246835
chr761988156199072E07247133
chr761991876199342E07247505
chr761993446199454E07247662
chr761995716200285E07247889
chr761467206146852E073-4830
chr761980076198097E07346325
chr761981226198311E07346440
chr761984016198502E07346719
chr761985176198637E07346835
chr761988156199072E07347133
chr761991876199342E07347505
chr761993446199454E07347662
chr761995716200285E07347889
chr761467206146852E074-4830
chr761469046146948E074-4734
chr761980076198097E07446325
chr761981226198311E07446440
chr761984016198502E07446719
chr761985176198637E07446835
chr761988156199072E07447133
chr761991876199342E07447505
chr761425596142738E081-8944
chr761427506142819E081-8863
chr761430086143116E081-8566
chr761431946143357E081-8325
chr761995716200285E08147889
chr761467206146852E082-4830
chr761469046146948E082-4734
chr761984016198502E08246719
chr761985176198637E08246835
chr761988156199072E08247133
chr761991876199342E08247505
chr761993446199454E08247662
chr761995716200285E08247889










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr761198876121751E067-29931
chr761434206143778E067-7904
chr761439536144846E067-6836
chr761448726146658E067-5024
chr761198876121751E068-29931
chr761434206143778E068-7904
chr761439536144846E068-6836
chr761448726146658E068-5024
chr761198876121751E069-29931
chr761434206143778E069-7904
chr761439536144846E069-6836
chr761448726146658E069-5024
chr761198876121751E070-29931
chr761434206143778E070-7904
chr761439536144846E070-6836
chr761448726146658E070-5024
chr761198876121751E071-29931
chr761434206143778E071-7904
chr761439536144846E071-6836
chr761448726146658E071-5024
chr761198876121751E072-29931
chr761434206143778E072-7904
chr761439536144846E072-6836
chr761448726146658E072-5024
chr761198876121751E073-29931
chr761434206143778E073-7904
chr761439536144846E073-6836
chr761448726146658E073-5024
chr761198876121751E074-29931
chr761434206143778E074-7904
chr761439536144846E074-6836
chr761448726146658E074-5024
chr761198876121751E081-29931
chr761448726146658E081-5024
chr761198876121751E082-29931
chr761434206143778E082-7904
chr761439536144846E082-6836
chr761448726146658E082-5024