rs1978888

Homo sapiens
T>C
PLCL1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0461 (13804/29888,GnomAD)
C=0488 (14216/29118,TOPMED)
C=0449 (2249/5008,1000G)
T==0494 (1902/3854,ALSPAC)
C=0496 (1841/3708,TWINSUK)
chr2:198024521 (GRCh38.p7) (2q33.1)
AD
GWASdb2
1   publication(s)
See rs on genome
133 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.198024521T>C
GRCh37.p13 chr 2NC_000002.11:g.198889245T>C

Gene: PLCL1, phospholipase C like 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PLCL1 transcriptNM_006226.3:c.N/AIntron Variant
PLCL1 transcript variant X1XM_005246643.3:c.N/AIntron Variant
PLCL1 transcript variant X3XM_011511351.2:c.N/AIntron Variant
PLCL1 transcript variant X2XM_017004339.1:c.N/AIntron Variant
PLCL1 transcript variant X5XM_017004340.1:c.N/AIntron Variant
PLCL1 transcript variant X4XM_005246644.3:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.508C=0.492
1000GenomesAmericanSub694T=0.580C=0.420
1000GenomesEast AsianSub1008T=0.780C=0.220
1000GenomesEuropeSub1006T=0.454C=0.546
1000GenomesGlobalStudy-wide5008T=0.551C=0.449
1000GenomesSouth AsianSub978T=0.450C=0.550
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.494C=0.506
The Genome Aggregation DatabaseAfricanSub8698T=0.498C=0.502
The Genome Aggregation DatabaseAmericanSub834T=0.660C=0.340
The Genome Aggregation DatabaseEast AsianSub1620T=0.803C=0.197
The Genome Aggregation DatabaseEuropeSub18434T=0.529C=0.470
The Genome Aggregation DatabaseGlobalStudy-wide29888T=0.538C=0.461
The Genome Aggregation DatabaseOtherSub302T=0.480C=0.520
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.511C=0.488
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.504C=0.496
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
rs19788881.15E-05alcohol consumption23743675

eQTL of rs1978888 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:198889245SF3B1ENSG00000115524.11T>C7.6222e-4589430Caudate_basal_ganglia

meQTL of rs1978888 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 )
chr2198849914198850263E067-38982
chr2198859584198859710E067-29535
chr2198860594198860652E067-28593
chr2198861601198861700E067-27545
chr2198861897198861982E067-27263
chr2198862039198862206E067-27039
chr2198862262198862312E067-26933
chr2198863014198863054E067-26191
chr2198895311198895383E0676066
chr2198905291198905433E06716046
chr2198918578198918696E06729333
chr2198860594198860652E068-28593
chr2198861601198861700E068-27545
chr2198861897198861982E068-27263
chr2198869628198869727E068-19518
chr2198869765198869846E068-19399
chr2198894292198894356E0685047
chr2198905291198905433E06816046
chr2198905500198905702E06816255
chr2198919509198919737E06830264
chr2198919820198920207E06830575
chr2198920560198920776E06831315
chr2198922587198922655E06833342
chr2198930117198930438E06840872
chr2198849914198850263E069-38982
chr2198860594198860652E069-28593
chr2198861601198861700E069-27545
chr2198869765198869846E069-19399
chr2198870058198870605E069-18640
chr2198881929198882001E069-7244
chr2198895156198895261E0695911
chr2198895311198895383E0696066
chr2198895428198895521E0696183
chr2198902752198902963E06913507
chr2198905291198905433E06916046
chr2198905500198905702E06916255
chr2198906774198907233E06917529
chr2198917564198917745E06928319
chr2198917974198918065E06928729
chr2198918578198918696E06929333
chr2198930117198930438E06940872
chr2198894809198894947E0705564
chr2198896952198897006E0707707
chr2198898314198898364E0709069
chr2198920560198920776E07031315
chr2198849914198850263E071-38982
chr2198858638198858821E071-30424
chr2198860594198860652E071-28593
chr2198861601198861700E071-27545
chr2198861897198861982E071-27263
chr2198862039198862206E071-27039
chr2198862262198862312E071-26933
chr2198869003198869098E071-20147
chr2198869628198869727E071-19518
chr2198869765198869846E071-19399
chr2198894292198894356E0715047
chr2198894442198894522E0715197
chr2198894809198894947E0715564
chr2198902752198902963E07113507
chr2198903313198903359E07114068
chr2198905291198905433E07116046
chr2198905500198905702E07116255
chr2198906774198907233E07117529
chr2198917564198917745E07128319
chr2198917974198918065E07128729
chr2198918578198918696E07129333
chr2198919150198919308E07129905
chr2198919509198919737E07130264
chr2198919820198920207E07130575
chr2198920560198920776E07131315
chr2198925168198925266E07135923
chr2198930117198930438E07140872
chr2198931481198931548E07142236
chr2198849914198850263E072-38982
chr2198860594198860652E072-28593
chr2198861601198861700E072-27545
chr2198861897198861982E072-27263
chr2198862039198862206E072-27039
chr2198862262198862312E072-26933
chr2198870058198870605E072-18640
chr2198881929198882001E072-7244
chr2198895428198895521E0726183
chr2198902752198902963E07213507
chr2198905291198905433E07216046
chr2198905500198905702E07216255
chr2198914419198914505E07225174
chr2198917974198918065E07228729
chr2198918578198918696E07229333
chr2198919150198919308E07229905
chr2198919509198919737E07230264
chr2198919820198920207E07230575
chr2198920560198920776E07231315
chr2198922587198922655E07233342
chr2198925168198925266E07235923
chr2198860594198860652E073-28593
chr2198861601198861700E073-27545
chr2198869628198869727E073-19518
chr2198869765198869846E073-19399
chr2198870058198870605E073-18640
chr2198918578198918696E07329333
chr2198919150198919308E07329905
chr2198919509198919737E07330264
chr2198849914198850263E074-38982
chr2198860594198860652E074-28593
chr2198861601198861700E074-27545
chr2198861897198861982E074-27263
chr2198862039198862206E074-27039
chr2198862262198862312E074-26933
chr2198863014198863054E074-26191
chr2198868844198868923E074-20322
chr2198869003198869098E074-20147
chr2198869628198869727E074-19518
chr2198869765198869846E074-19399
chr2198881929198882001E074-7244
chr2198894292198894356E0745047
chr2198894442198894522E0745197
chr2198894809198894947E0745564
chr2198895156198895261E0745911
chr2198895311198895383E0746066
chr2198902752198902963E07413507
chr2198905291198905433E07416046
chr2198905500198905702E07416255
chr2198906774198907233E07417529
chr2198917564198917745E07428319
chr2198917974198918065E07428729
chr2198918578198918696E07429333
chr2198919150198919308E07429905
chr2198919509198919737E07430264
chr2198919820198920207E07430575
chr2198920560198920776E07431315
chr2198930117198930438E07440872
chr2198931481198931548E07442236
chr2198849914198850263E082-38982