rs2540089

Homo sapiens
C>T
None
Check p-value
SNV (Single Nucleotide Variation)
T=0306 (9126/29794,GnomAD)
T=0329 (9602/29116,TOPMED)
T=0374 (1873/5008,1000G)
T=0306 (1178/3854,ALSPAC)
T=0311 (1153/3708,TWINSUK)
chr2:59535236 (GRCh38.p7) (2p16.1)
AD
GWASdb2
1   publication(s)
See rs on genome
15 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.59535236C>T
GRCh37.p13 chr 2NC_000002.11:g.59762371C>T

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.651T=0.349
1000GenomesAmericanSub694C=0.600T=0.400
1000GenomesEast AsianSub1008C=0.480T=0.520
1000GenomesEuropeSub1006C=0.692T=0.308
1000GenomesGlobalStudy-wide5008C=0.626T=0.374
1000GenomesSouth AsianSub978C=0.700T=0.300
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.694T=0.306
The Genome Aggregation DatabaseAfricanSub8662C=0.673T=0.327
The Genome Aggregation DatabaseAmericanSub838C=0.580T=0.420
The Genome Aggregation DatabaseEast AsianSub1606C=0.477T=0.523
The Genome Aggregation DatabaseEuropeSub18388C=0.727T=0.272
The Genome Aggregation DatabaseGlobalStudy-wide29794C=0.693T=0.306
The Genome Aggregation DatabaseOtherSub300C=0.680T=0.320
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.670T=0.329
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.689T=0.311
PMID Title Author Journal
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs25400895.45E-05alcohol consumption23743675

eQTL of rs2540089 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 rs2540089 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 )
chr25981223659812346E07049865
chr25979357059793733E08131199
chr25979377559794244E08131404
chr25979429459794429E08131923
chr25979448259795096E08132111
chr25979531859795414E08132947
chr25979556659795892E08133195
chr25979831859798751E08135947
chr25979946259799668E08137091
chr25979357059793733E08231199
chr25979377559794244E08231404
chr25979429459794429E08231923
chr25979448259795096E08232111
chr25979531859795414E08232947
chr25981223659812346E08249865