rs2540088

Homo sapiens
C>A / C>G
None
Check p-value
SNV (Single Nucleotide Variation)
G=0306 (9170/29926,GnomAD)
G=0329 (9596/29116,TOPMED)
G=0373 (1869/5008,1000G)
G=0304 (1171/3854,ALSPAC)
G=0311 (1153/3708,TWINSUK)
chr2:59535425 (GRCh38.p7) (2p16.1)
AD
GWASdb2
1   publication(s)
See rs on genome
138 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.59535425C>A
GRCh38.p7 chr 2NC_000002.12:g.59535425C>G
GRCh37.p13 chr 2NC_000002.11:g.59762560C>A
GRCh37.p13 chr 2NC_000002.11:g.59762560C>G

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.651G=0.349
1000GenomesAmericanSub694C=0.600G=0.400
1000GenomesEast AsianSub1008C=0.483G=0.517
1000GenomesEuropeSub1006C=0.693G=0.307
1000GenomesGlobalStudy-wide5008C=0.627G=0.373
1000GenomesSouth AsianSub978C=0.700G=0.300
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.696G=0.304
The Genome Aggregation DatabaseAfricanSub8708C=0.674G=0.326
The Genome Aggregation DatabaseAmericanSub838C=0.580G=0.42,
The Genome Aggregation DatabaseEast AsianSub1614C=0.470G=0.530
The Genome Aggregation DatabaseEuropeSub18464C=0.727G=0.272
The Genome Aggregation DatabaseGlobalStudy-wide29926C=0.693G=0.306
The Genome Aggregation DatabaseOtherSub302C=0.680G=0.32,
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.670G=0.329
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.689G=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
rs25400884.87E-05alcohol consumption23743675

eQTL of rs2540088 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 rs2540088 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 )
chr221069782107379E067-8423
chr221074582107755E067-8047
chr221108212110957E067-4845
chr221110002111262E067-4540
chr221162462116722E067444
chr221167672116852E067965
chr221497292149842E06733927
chr221505862150636E06734784
chr221507612150936E06734959
chr221509682151945E06735166
chr221064712106603E068-9199
chr221067692106976E068-8826
chr221069782107379E068-8423
chr221074582107755E068-8047
chr221108212110957E068-4845
chr221110002111262E068-4540
chr221162462116722E068444
chr221167672116852E068965
chr221171882117240E0681386
chr221173592117465E0681557
chr221497292149842E06833927
chr221505862150636E06834784
chr221507612150936E06834959
chr221509682151945E06835166
chr221521162152174E06836314
chr221069782107379E069-8423
chr221074582107755E069-8047
chr221108212110957E069-4845
chr221110002111262E069-4540
chr221115292111742E069-4060
chr221505862150636E06934784
chr221507612150936E06934959
chr221509682151945E06935166
chr221521162152174E06936314
chr221069782107379E070-8423
chr221074582107755E070-8047
chr221108212110957E070-4845
chr221110002111262E070-4540
chr221115292111742E070-4060
chr221313212131590E07015519
chr221354132135493E07019611
chr221505862150636E07034784
chr221521162152174E07036314
chr221527622152826E07036960
chr221067692106976E071-8826
chr221074582107755E071-8047
chr221110002111262E071-4540
chr221115292111742E071-4060
chr221505862150636E07134784
chr221507612150936E07134959
chr221509682151945E07135166
chr221067692106976E072-8826
chr221074582107755E072-8047
chr221108212110957E072-4845
chr221110002111262E072-4540
chr221115292111742E072-4060
chr221162462116722E072444
chr221167672116852E072965
chr221505862150636E07234784
chr221507612150936E07234959
chr221509682151945E07235166
chr221521162152174E07236314
chr221069782107379E073-8423
chr221074582107755E073-8047
chr221108212110957E073-4845
chr221110002111262E073-4540
chr221115292111742E073-4060
chr221162462116722E073444
chr221167672116852E073965
chr221171882117240E0731386
chr221173592117465E0731557
chr221313212131590E07315519
chr221505862150636E07334784
chr221507612150936E07334959
chr221509682151945E07335166
chr221521162152174E07336314
chr221069782107379E074-8423
chr221074582107755E074-8047
chr221108212110957E074-4845
chr221110002111262E074-4540
chr221115292111742E074-4060
chr221497292149842E07433927
chr221505862150636E07434784
chr221507612150936E07434959
chr221509682151945E07435166
chr221058352105938E081-9864
chr221059432106025E081-9777
chr221064712106603E081-9199
chr221067692106976E081-8826
chr221069782107379E081-8423
chr221074582107755E081-8047
chr221108212110957E081-4845
chr221110002111262E081-4540
chr221115292111742E081-4060
chr221131662113282E081-2520
chr221133932113443E081-2359
chr221135202113618E081-2184
chr221137122113936E081-1866
chr221246932124869E0818891
chr221249132124981E0819111
chr221313212131590E08115519
chr221354132135493E08119611
chr221497292149842E08133927
chr221505862150636E08134784
chr221507612150936E08134959
chr221509682151945E08135166
chr221521162152174E08136314
chr221527622152826E08136960
chr221548462154917E08139044
chr221551772155331E08139375
chr221562422156566E08140440
chr221619832162315E08146181
chr221623832162441E08146581
chr221625342162592E08146732
chr221627392162789E08146937
chr221632042163267E08147402
chr221634792163523E08147677
chr220886932088745E082-27057
chr221058352105938E082-9864
chr221059432106025E082-9777
chr221064712106603E082-9199
chr221067692106976E082-8826
chr221074582107755E082-8047
chr221110002111262E082-4540
chr221115292111742E082-4060
chr221131662113282E082-2520
chr221133932113443E082-2359
chr221135202113618E082-2184
chr221137122113936E082-1866
chr221313212131590E08215519
chr221354132135493E08219611
chr221497292149842E08233927
chr221505862150636E08234784
chr221521162152174E08236314
chr221527622152826E08236960
chr221562422156566E08240440
chr221627392162789E08246937
chr221632042163267E08247402