rs56265469

Homo sapiens
C>T
UTP20 : Synonymous Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0248 (30154/121256,ExAC)
T=0221 (6619/29916,GnomAD)
T=0226 (6592/29118,TOPMED)
C==0218 (2842/13002,GO-ESP)
T=0257 (1285/5008,1000G)
T=0229 (882/3854,ALSPAC)
T=0232 (859/3708,TWINSUK)
chr12:101338877 (GRCh38.p7) (12q23.2)
AD
GWASdb2
1   publication(s)
See rs on genome
9 Enhancers around
16 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.101338877C>T
GRCh37.p13 chr 12NC_000012.11:g.101732655C>T

Gene: UTP20, UTP20, small subunit processome component(plus strand)

Molecule type Change Amino acid[Codon] SO Term
UTP20 transcriptNM_014503.2:c.393...NM_014503.2:c.3933C>TS [AGC]> S [AGT]Coding Sequence Variant
small subunit processome component 20 homologNP_055318.2:p.Ser...NP_055318.2:p.Ser1311=S [Ser]> S [Ser]Synonymous Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.846T=0.154
1000GenomesAmericanSub694C=0.680T=0.320
1000GenomesEast AsianSub1008C=0.625T=0.375
1000GenomesEuropeSub1006C=0.762T=0.238
1000GenomesGlobalStudy-wide5008C=0.743T=0.257
1000GenomesSouth AsianSub978C=0.750T=0.250
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.771T=0.229
The Exome Aggregation ConsortiumAmericanSub21948C=0.730T=0.270
The Exome Aggregation ConsortiumAsianSub25150C=0.710T=0.289
The Exome Aggregation ConsortiumEuropeSub73252C=0.771T=0.228
The Exome Aggregation ConsortiumGlobalStudy-wide121256C=0.751T=0.248
The Exome Aggregation ConsortiumOtherSub906C=0.730T=0.270
The Genome Aggregation DatabaseAfricanSub8720C=0.828T=0.172
The Genome Aggregation DatabaseAmericanSub836C=0.660T=0.340
The Genome Aggregation DatabaseEast AsianSub1610C=0.644T=0.356
The Genome Aggregation DatabaseEuropeSub18450C=0.773T=0.226
The Genome Aggregation DatabaseGlobalStudy-wide29916C=0.778T=0.221
The Genome Aggregation DatabaseOtherSub300C=0.710T=0.290
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.773T=0.226
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.768T=0.232
PMID Title Author Journal
24962325Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.Kapoor MDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs562654691.25E-07alcohol dependence (age at onset)24962325

eQTL of rs56265469 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 rs56265469 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 )
chr12101691390101691641E067-41014
chr12101692002101692211E067-40444
chr12101692243101692491E067-40164
chr12101692002101692211E069-40444
chr12101692243101692491E069-40164
chr12101684127101684167E071-48488
chr12101691390101691641E071-41014
chr12101691390101691641E072-41014
chr12101692002101692211E072-40444




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr12101692853101693016E067-39639
chr12101693076101693399E067-39256
chr12101693724101694082E067-38573
chr12101692853101693016E068-39639
chr12101693076101693399E068-39256
chr12101692853101693016E069-39639
chr12101693076101693399E069-39256
chr12101693724101694082E069-38573
chr12101692853101693016E071-39639
chr12101693076101693399E071-39256
chr12101693724101694082E071-38573
chr12101692853101693016E072-39639
chr12101693076101693399E072-39256
chr12101692853101693016E074-39639
chr12101693076101693399E074-39256
chr12101693724101694082E074-38573