rs6738825

Homo sapiens
A>G
PLCL1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0497 (14495/29118,TOPMED)
G=0454 (2274/5008,1000G)
A==0494 (1902/3854,ALSPAC)
G=0496 (1841/3708,TWINSUK)
chr2:198032171 (GRCh38.p7) (2q33.1)
AD
GWASdb2
9   publication(s)
See rs on genome
140 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.198032171A>G
GRCh37.p13 chr 2NC_000002.11:g.198896895A>G

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
1000GenomesAfricanSub1322A=0.491G=0.509
1000GenomesAmericanSub694A=0.570G=0.430
1000GenomesEast AsianSub1008A=0.780G=0.220
1000GenomesEuropeSub1006A=0.454G=0.546
1000GenomesGlobalStudy-wide5008A=0.546G=0.454
1000GenomesSouth AsianSub978A=0.450G=0.550
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.494G=0.506
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.502G=0.497
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.504G=0.496
PMID Title Author Journal
27336838Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci.Di Narzo AFClin Transl Gastroenterol
22174698A comprehensive analysis of shared loci between systemic lupus erythematosus (SLE) and sixteen autoimmune diseases reveals limited genetic overlap.Ramos PSPLoS Genet
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet
21102463Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.Franke ANat Genet
22544929IRF5 risk polymorphisms contribute to interindividual variance in pattern recognition receptor-mediated cytokine secretion in human monocyte-derived cells.Hedl MJ Immunol
23817569A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.Hinds DANat Genet
23983088Genome-wide association study of dermatomyositis reveals genetic overlap with other autoimmune disorders.Miller FWArthritis Rheum
26603167Positive association of genetic variations in the phospholipase C-like 1 gene with dermatomyositis in Chinese Han.Wang QImmunol Res
24956270Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants.Narahara MPLoS One

P-Value

SNP ID p-value Traits Study
rs67388251.1E-05alcohol consumption23743675

eQTL of rs6738825 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr2:198896895SF3B1ENSG00000115524.11A>G7.6222e-4597080Caudate_basal_ganglia

meQTL of rs6738825 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 )
chr2198849914198850263E067-46632
chr2198859584198859710E067-37185
chr2198860594198860652E067-36243
chr2198861601198861700E067-35195
chr2198861897198861982E067-34913
chr2198862039198862206E067-34689
chr2198862262198862312E067-34583
chr2198863014198863054E067-33841
chr2198895311198895383E067-1512
chr2198905291198905433E0678396
chr2198918578198918696E06721683
chr2198945273198945529E06748378
chr2198860594198860652E068-36243
chr2198861601198861700E068-35195
chr2198861897198861982E068-34913
chr2198869628198869727E068-27168
chr2198869765198869846E068-27049
chr2198894292198894356E068-2539
chr2198905291198905433E0688396
chr2198905500198905702E0688605
chr2198919509198919737E06822614
chr2198919820198920207E06822925
chr2198920560198920776E06823665
chr2198922587198922655E06825692
chr2198930117198930438E06833222
chr2198945273198945529E06848378
chr2198849914198850263E069-46632
chr2198860594198860652E069-36243
chr2198861601198861700E069-35195
chr2198869765198869846E069-27049
chr2198870058198870605E069-26290
chr2198881929198882001E069-14894
chr2198895156198895261E069-1634
chr2198895311198895383E069-1512
chr2198895428198895521E069-1374
chr2198902752198902963E0695857
chr2198905291198905433E0698396
chr2198905500198905702E0698605
chr2198906774198907233E0699879
chr2198917564198917745E06920669
chr2198917974198918065E06921079
chr2198918578198918696E06921683
chr2198930117198930438E06933222
chr2198945273198945529E06948378
chr2198894809198894947E070-1948
chr2198896952198897006E07057
chr2198898314198898364E0701419
chr2198920560198920776E07023665
chr2198849914198850263E071-46632
chr2198858638198858821E071-38074
chr2198860594198860652E071-36243
chr2198861601198861700E071-35195
chr2198861897198861982E071-34913
chr2198862039198862206E071-34689
chr2198862262198862312E071-34583
chr2198869003198869098E071-27797
chr2198869628198869727E071-27168
chr2198869765198869846E071-27049
chr2198894292198894356E071-2539
chr2198894442198894522E071-2373
chr2198894809198894947E071-1948
chr2198902752198902963E0715857
chr2198903313198903359E0716418
chr2198905291198905433E0718396
chr2198905500198905702E0718605
chr2198906774198907233E0719879
chr2198917564198917745E07120669
chr2198917974198918065E07121079
chr2198918578198918696E07121683
chr2198919150198919308E07122255
chr2198919509198919737E07122614
chr2198919820198920207E07122925
chr2198920560198920776E07123665
chr2198925168198925266E07128273
chr2198930117198930438E07133222
chr2198931481198931548E07134586
chr2198945273198945529E07148378
chr2198849914198850263E072-46632
chr2198860594198860652E072-36243
chr2198861601198861700E072-35195
chr2198861897198861982E072-34913
chr2198862039198862206E072-34689
chr2198862262198862312E072-34583
chr2198870058198870605E072-26290
chr2198881929198882001E072-14894
chr2198895428198895521E072-1374
chr2198902752198902963E0725857
chr2198905291198905433E0728396
chr2198905500198905702E0728605
chr2198914419198914505E07217524
chr2198917974198918065E07221079
chr2198918578198918696E07221683
chr2198919150198919308E07222255
chr2198919509198919737E07222614
chr2198919820198920207E07222925
chr2198920560198920776E07223665
chr2198922587198922655E07225692
chr2198925168198925266E07228273
chr2198945273198945529E07248378
chr2198860594198860652E073-36243
chr2198861601198861700E073-35195
chr2198869628198869727E073-27168
chr2198869765198869846E073-27049
chr2198870058198870605E073-26290
chr2198918578198918696E07321683
chr2198919150198919308E07322255
chr2198919509198919737E07322614
chr2198849914198850263E074-46632
chr2198860594198860652E074-36243
chr2198861601198861700E074-35195
chr2198861897198861982E074-34913
chr2198862039198862206E074-34689
chr2198862262198862312E074-34583
chr2198863014198863054E074-33841
chr2198868844198868923E074-27972
chr2198869003198869098E074-27797
chr2198869628198869727E074-27168
chr2198869765198869846E074-27049
chr2198881929198882001E074-14894
chr2198894292198894356E074-2539
chr2198894442198894522E074-2373
chr2198894809198894947E074-1948
chr2198895156198895261E074-1634
chr2198895311198895383E074-1512
chr2198902752198902963E0745857
chr2198905291198905433E0748396
chr2198905500198905702E0748605
chr2198906774198907233E0749879
chr2198917564198917745E07420669
chr2198917974198918065E07421079
chr2198918578198918696E07421683
chr2198919150198919308E07422255
chr2198919509198919737E07422614
chr2198919820198920207E07422925
chr2198920560198920776E07423665
chr2198930117198930438E07433222
chr2198931481198931548E07434586
chr2198945273198945529E07448378
chr2198945273198945529E08148378
chr2198849914198850263E082-46632