rs9973400

Homo sapiens
T>C
PLCL1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0494 (14779/29916,GnomAD)
T==0441 (12848/29118,TOPMED)
T==0497 (2491/5008,1000G)
T==0481 (1855/3854,ALSPAC)
T==0490 (1817/3708,TWINSUK)
chr2:198076854 (GRCh38.p7) (2q33.1)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.198076854T>C
GRCh37.p13 chr 2NC_000002.11:g.198941578T>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 X4XM_005246644.3: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

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.369C=0.631
1000GenomesAmericanSub694T=0.550C=0.450
1000GenomesEast AsianSub1008T=0.774C=0.226
1000GenomesEuropeSub1006T=0.449C=0.551
1000GenomesGlobalStudy-wide5008T=0.497C=0.503
1000GenomesSouth AsianSub978T=0.400C=0.600
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.481C=0.519
The Genome Aggregation DatabaseAfricanSub8694T=0.375C=0.625
The Genome Aggregation DatabaseAmericanSub828T=0.640C=0.360
The Genome Aggregation DatabaseEast AsianSub1620T=0.804C=0.196
The Genome Aggregation DatabaseEuropeSub18472T=0.516C=0.483
The Genome Aggregation DatabaseGlobalStudy-wide29916T=0.494C=0.506
The Genome Aggregation DatabaseOtherSub302T=0.470C=0.530
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.441C=0.558
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.490C=0.510
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
rs99734008.29E-06alcohol consumption23743675

eQTL of rs9973400 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 rs9973400 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 )
chr2198895311198895383E067-46195
chr2198905291198905433E067-36145
chr2198918578198918696E067-22882
chr2198945273198945529E0673695
chr2198961450198961502E06719872
chr2198961841198961912E06720263
chr2198962411198962470E06720833
chr2198963763198963935E06722185
chr2198965149198965308E06723571
chr2198975540198975603E06733962
chr2198978077198978371E06736499
chr2198894292198894356E068-47222
chr2198905291198905433E068-36145
chr2198905500198905702E068-35876
chr2198919509198919737E068-21841
chr2198919820198920207E068-21371
chr2198920560198920776E068-20802
chr2198922587198922655E068-18923
chr2198930117198930438E068-11140
chr2198945273198945529E0683695
chr2198961841198961912E06820263
chr2198965149198965308E06823571
chr2198895156198895261E069-46317
chr2198895311198895383E069-46195
chr2198895428198895521E069-46057
chr2198902752198902963E069-38615
chr2198905291198905433E069-36145
chr2198905500198905702E069-35876
chr2198906774198907233E069-34345
chr2198917564198917745E069-23833
chr2198917974198918065E069-23513
chr2198918578198918696E069-22882
chr2198930117198930438E069-11140
chr2198945273198945529E0693695
chr2198961841198961912E06920263
chr2198962411198962470E06920833
chr2198963763198963935E06922185
chr2198965149198965308E06923571
chr2198975540198975603E06933962
chr2198978425198978498E06936847
chr2198989790198989843E06948212
chr2198989886198989996E06948308
chr2198894809198894947E070-46631
chr2198896952198897006E070-44572
chr2198898314198898364E070-43214
chr2198920560198920776E070-20802
chr2198894292198894356E071-47222
chr2198894442198894522E071-47056
chr2198894809198894947E071-46631
chr2198902752198902963E071-38615
chr2198903313198903359E071-38219
chr2198905291198905433E071-36145
chr2198905500198905702E071-35876
chr2198906774198907233E071-34345
chr2198917564198917745E071-23833
chr2198917974198918065E071-23513
chr2198918578198918696E071-22882
chr2198919150198919308E071-22270
chr2198919509198919737E071-21841
chr2198919820198920207E071-21371
chr2198920560198920776E071-20802
chr2198925168198925266E071-16312
chr2198930117198930438E071-11140
chr2198931481198931548E071-10030
chr2198945273198945529E0713695
chr2198960865198960964E07119287
chr2198961450198961502E07119872
chr2198961841198961912E07120263
chr2198962411198962470E07120833
chr2198963763198963935E07122185
chr2198965149198965308E07123571
chr2198975540198975603E07133962
chr2198977050198977114E07135472
chr2198981402198981945E07139824
chr2198982067198982154E07140489
chr2198982183198982417E07140605
chr2198895428198895521E072-46057
chr2198902752198902963E072-38615
chr2198905291198905433E072-36145
chr2198905500198905702E072-35876
chr2198914419198914505E072-27073
chr2198917974198918065E072-23513
chr2198918578198918696E072-22882
chr2198919150198919308E072-22270
chr2198919509198919737E072-21841
chr2198919820198920207E072-21371
chr2198920560198920776E072-20802
chr2198922587198922655E072-18923
chr2198925168198925266E072-16312
chr2198945273198945529E0723695
chr2198961841198961912E07220263
chr2198962411198962470E07220833
chr2198965149198965308E07223571
chr2198975540198975603E07233962
chr2198977050198977114E07235472
chr2198978077198978371E07236499
chr2198989790198989843E07248212
chr2198989886198989996E07248308
chr2198918578198918696E073-22882
chr2198919150198919308E073-22270
chr2198919509198919737E073-21841
chr2198962411198962470E07320833
chr2198965149198965308E07323571
chr2198894292198894356E074-47222
chr2198894442198894522E074-47056
chr2198894809198894947E074-46631
chr2198895156198895261E074-46317
chr2198895311198895383E074-46195
chr2198902752198902963E074-38615
chr2198905291198905433E074-36145
chr2198905500198905702E074-35876
chr2198906774198907233E074-34345
chr2198917564198917745E074-23833
chr2198917974198918065E074-23513
chr2198918578198918696E074-22882
chr2198919150198919308E074-22270
chr2198919509198919737E074-21841
chr2198919820198920207E074-21371
chr2198920560198920776E074-20802
chr2198930117198930438E074-11140
chr2198931481198931548E074-10030
chr2198945273198945529E0743695
chr2198961841198961912E07420263
chr2198962411198962470E07420833
chr2198963763198963935E07422185
chr2198965149198965308E07423571
chr2198975540198975603E07433962
chr2198978077198978371E07436499
chr2198978425198978498E07436847
chr2198978866198979373E07437288
chr2198979410198979460E07437832
chr2198979807198979926E07438229
chr2198980083198980143E07438505
chr2198984220198984270E07442642
chr2198945273198945529E0813695