rs2117339

Homo sapiens
C>T
PLCL1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0403 (12078/29936,GnomAD)
T=0400 (11647/29118,TOPMED)
T=0387 (1939/5008,1000G)
C==0489 (1884/3854,ALSPAC)
C==0496 (1839/3708,TWINSUK)
chr2:198051010 (GRCh38.p7) (2q33.1)
AD
GWASdb2
4   publication(s)
See rs on genome
129 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.198051010C>T
GRCh37.p13 chr 2NC_000002.11:g.198915734C>T

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
1000GenomesAfricanSub1322C=0.761T=0.239
1000GenomesAmericanSub694C=0.590T=0.410
1000GenomesEast AsianSub1008C=0.778T=0.222
1000GenomesEuropeSub1006C=0.449T=0.551
1000GenomesGlobalStudy-wide5008C=0.613T=0.387
1000GenomesSouth AsianSub978C=0.430T=0.570
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.489T=0.511
The Genome Aggregation DatabaseAfricanSub8722C=0.713T=0.287
The Genome Aggregation DatabaseAmericanSub838C=0.670T=0.330
The Genome Aggregation DatabaseEast AsianSub1618C=0.804T=0.196
The Genome Aggregation DatabaseEuropeSub18456C=0.521T=0.478
The Genome Aggregation DatabaseGlobalStudy-wide29936C=0.596T=0.403
The Genome Aggregation DatabaseOtherSub302C=0.480T=0.520
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.600T=0.400
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.496T=0.504
PMID Title Author Journal
26603167Positive association of genetic variations in the phospholipase C-like 1 gene with dermatomyositis in Chinese Han.Wang QImmunol Res
23817569A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.Hinds DANat Genet
27506385Predicting gene targets from integrative analyses of summary data from GWAS and eQTL studies for 28 human complex traits.Pavlides JMGenome Med
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
rs21173394.4E-06alcohol consumption23743675

eQTL of rs2117339 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 rs2117339 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 )
chr2198895311198895383E067-20351
chr2198905291198905433E067-10301
chr2198918578198918696E0672844
chr2198945273198945529E06729539
chr2198961450198961502E06745716
chr2198961841198961912E06746107
chr2198962411198962470E06746677
chr2198963763198963935E06748029
chr2198965149198965308E06749415
chr2198869628198869727E068-46007
chr2198869765198869846E068-45888
chr2198894292198894356E068-21378
chr2198905291198905433E068-10301
chr2198905500198905702E068-10032
chr2198919509198919737E0683775
chr2198919820198920207E0684086
chr2198920560198920776E0684826
chr2198922587198922655E0686853
chr2198930117198930438E06814383
chr2198945273198945529E06829539
chr2198961841198961912E06846107
chr2198965149198965308E06849415
chr2198869765198869846E069-45888
chr2198870058198870605E069-45129
chr2198881929198882001E069-33733
chr2198895156198895261E069-20473
chr2198895311198895383E069-20351
chr2198895428198895521E069-20213
chr2198902752198902963E069-12771
chr2198905291198905433E069-10301
chr2198905500198905702E069-10032
chr2198906774198907233E069-8501
chr2198917564198917745E0691830
chr2198917974198918065E0692240
chr2198918578198918696E0692844
chr2198930117198930438E06914383
chr2198945273198945529E06929539
chr2198961841198961912E06946107
chr2198962411198962470E06946677
chr2198963763198963935E06948029
chr2198965149198965308E06949415
chr2198894809198894947E070-20787
chr2198896952198897006E070-18728
chr2198898314198898364E070-17370
chr2198920560198920776E0704826
chr2198869003198869098E071-46636
chr2198869628198869727E071-46007
chr2198869765198869846E071-45888
chr2198894292198894356E071-21378
chr2198894442198894522E071-21212
chr2198894809198894947E071-20787
chr2198902752198902963E071-12771
chr2198903313198903359E071-12375
chr2198905291198905433E071-10301
chr2198905500198905702E071-10032
chr2198906774198907233E071-8501
chr2198917564198917745E0711830
chr2198917974198918065E0712240
chr2198918578198918696E0712844
chr2198919150198919308E0713416
chr2198919509198919737E0713775
chr2198919820198920207E0714086
chr2198920560198920776E0714826
chr2198925168198925266E0719434
chr2198930117198930438E07114383
chr2198931481198931548E07115747
chr2198945273198945529E07129539
chr2198960865198960964E07145131
chr2198961450198961502E07145716
chr2198961841198961912E07146107
chr2198962411198962470E07146677
chr2198963763198963935E07148029
chr2198965149198965308E07149415
chr2198870058198870605E072-45129
chr2198881929198882001E072-33733
chr2198895428198895521E072-20213
chr2198902752198902963E072-12771
chr2198905291198905433E072-10301
chr2198905500198905702E072-10032
chr2198914419198914505E072-1229
chr2198917974198918065E0722240
chr2198918578198918696E0722844
chr2198919150198919308E0723416
chr2198919509198919737E0723775
chr2198919820198920207E0724086
chr2198920560198920776E0724826
chr2198922587198922655E0726853
chr2198925168198925266E0729434
chr2198945273198945529E07229539
chr2198961841198961912E07246107
chr2198962411198962470E07246677
chr2198965149198965308E07249415
chr2198869628198869727E073-46007
chr2198869765198869846E073-45888
chr2198870058198870605E073-45129
chr2198918578198918696E0732844
chr2198919150198919308E0733416
chr2198919509198919737E0733775
chr2198962411198962470E07346677
chr2198965149198965308E07349415
chr2198868844198868923E074-46811
chr2198869003198869098E074-46636
chr2198869628198869727E074-46007
chr2198869765198869846E074-45888
chr2198881929198882001E074-33733
chr2198894292198894356E074-21378
chr2198894442198894522E074-21212
chr2198894809198894947E074-20787
chr2198895156198895261E074-20473
chr2198895311198895383E074-20351
chr2198902752198902963E074-12771
chr2198905291198905433E074-10301
chr2198905500198905702E074-10032
chr2198906774198907233E074-8501
chr2198917564198917745E0741830
chr2198917974198918065E0742240
chr2198918578198918696E0742844
chr2198919150198919308E0743416
chr2198919509198919737E0743775
chr2198919820198920207E0744086
chr2198920560198920776E0744826
chr2198930117198930438E07414383
chr2198931481198931548E07415747
chr2198945273198945529E07429539
chr2198961841198961912E07446107
chr2198962411198962470E07446677
chr2198963763198963935E07448029
chr2198965149198965308E07449415
chr2198945273198945529E08129539