rs2540099

Homo sapiens
C>T
None
Check p-value
SNV (Single Nucleotide Variation)
T=0300 (8985/29890,GnomAD)
T=0325 (9480/29116,TOPMED)
T=0370 (1852/5008,1000G)
T=0290 (1118/3854,ALSPAC)
T=0300 (1113/3708,TWINSUK)
chr2:59526606 (GRCh38.p7) (2p16.1)
AD
GWASdb2
1   publication(s)
See rs on genome
13 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.59526606C>T
GRCh37.p13 chr 2NC_000002.11:g.59753741C>T

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.651T=0.349
1000GenomesAmericanSub694C=0.570T=0.430
1000GenomesEast AsianSub1008C=0.489T=0.511
1000GenomesEuropeSub1006C=0.711T=0.289
1000GenomesGlobalStudy-wide5008C=0.630T=0.370
1000GenomesSouth AsianSub978C=0.710T=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.710T=0.290
The Genome Aggregation DatabaseAfricanSub8704C=0.675T=0.325
The Genome Aggregation DatabaseAmericanSub838C=0.550T=0.450
The Genome Aggregation DatabaseEast AsianSub1610C=0.488T=0.512
The Genome Aggregation DatabaseEuropeSub18436C=0.736T=0.263
The Genome Aggregation DatabaseGlobalStudy-wide29890C=0.699T=0.300
The Genome Aggregation DatabaseOtherSub302C=0.700T=0.300
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.674T=0.325
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.700T=0.300
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
rs25400996.37E-05alcohol consumption23743675

eQTL of rs2540099 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 rs2540099 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 )
chr25979357059793733E08139829
chr25979377559794244E08140034
chr25979429459794429E08140553
chr25979448259795096E08140741
chr25979531859795414E08141577
chr25979556659795892E08141825
chr25979831859798751E08144577
chr25979946259799668E08145721
chr25979357059793733E08239829
chr25979377559794244E08240034
chr25979429459794429E08240553
chr25979448259795096E08240741
chr25979531859795414E08241577