rs2117740

Homo sapiens
A>G
PDE11A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0495 (14811/29886,GnomAD)
G=0465 (13557/29118,TOPMED)
A==0450 (2252/5008,1000G)
A==0478 (1842/3854,ALSPAC)
A==0471 (1747/3708,TWINSUK)
chr2:178025602 (GRCh38.p7) (2q31.2)
AD
GWASdb2
1   publication(s)
See rs on genome
5 Enhancers around
6 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.178025602A>G
GRCh37.p13 chr 2NC_000002.11:g.178890329A>G
PDE11A RefSeqGeneNG_012168.1:g.87738T>C

Gene: PDE11A, phosphodiesterase 11A(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PDE11A transcript variant 3NM_001077197.1:c.N/AIntron Variant
PDE11A transcript variant 4NM_016953.3:c.N/AIntron Variant
PDE11A transcript variant 1NM_001077196.1:c.N/AGenic Upstream Transcript Variant
PDE11A transcript variant 2NM_001077358.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.633G=0.367
1000GenomesAmericanSub694A=0.340G=0.660
1000GenomesEast AsianSub1008A=0.303G=0.697
1000GenomesEuropeSub1006A=0.468G=0.532
1000GenomesGlobalStudy-wide5008A=0.450G=0.550
1000GenomesSouth AsianSub978A=0.420G=0.580
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.478G=0.522
The Genome Aggregation DatabaseAfricanSub8702A=0.632G=0.368
The Genome Aggregation DatabaseAmericanSub830A=0.300G=0.700
The Genome Aggregation DatabaseEast AsianSub1596A=0.293G=0.707
The Genome Aggregation DatabaseEuropeSub18456A=0.473G=0.526
The Genome Aggregation DatabaseGlobalStudy-wide29886A=0.504G=0.495
The Genome Aggregation DatabaseOtherSub302A=0.420G=0.580
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.534G=0.465
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.471G=0.529
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
rs21177406.43E-06alcohol dependence (age at onset)24962325

eQTL of rs2117740 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 rs2117740 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 )
chr2178873434178873654E067-16675
chr2178873434178873654E070-16675
chr2178936734178936810E07046405
chr2178873434178873654E081-16675
chr2178873434178873654E082-16675




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2178937095178938161E07046766
chr2178937095178938161E07146766
chr2178937095178938161E07246766
chr2178937095178938161E07346766
chr2178937095178938161E07446766
chr2178937095178938161E08246766