DOI: 10.5281/zenodo.17297439
title: Colocalization to identify sharing of genetic effects between eQTL-sQTL-edQTL in BigBrain dataset

description: QTL-QTL Colocalization: 

BigBrain_cis_eQTL_cis_edQTL_COLOC.tsv => (qtl1= eQTL and qtl2= RNA-editing; phenotype.qtl1= gene, phenotype.qtl2= editing site )

BigBrain_cis_eQTL_cis_sQTL_COLOC.tsv => (qtl1= eQTL and qtl2= splicing junction; phenotype.qtl1= gene, phenotype.qtl2= splicing junction)

BigBrain_cis_sQTL_cis_edQTL_COLOC.tsv => (qtl1= splicing junction and qtl2= RNA-editing; phenotype.qtl1= splicing junction, phenotype.qtl2= editing site)

Description:

Gene_ID: Ensembl or gene identifier associated with the tested QTL pair.phenotype.qtl1: Name or ID of the first molecular phenotype (e.g., gene or junction).QTL_SNP.qtl1: Lead SNP for phenotype 1.QTL_P.qtl1: Association P-value for phenotype 1.QTL_Beta.qtl1: Effect size (β) of the lead SNP on phenotype 1.QTL_SE.qtl1: Standard error of the effect size for phenotype 1.QTL_MAF.qtl1: Minor allele frequency of the lead SNP for phenotype 1.QTL_chr.qtl1: Chromosome of the lead SNP for phenotype 1.QTL_pos.qtl1: Genomic position (bp, hg38) of the lead SNP for phenotype 1.GWAS_SNP_Beta.qtl1: Corresponding GWAS beta value for that SNP if included for reference.GWAS_SNP_SE.qtl1: Standard error for the GWAS beta.GWAS_SNP_P.qtl1: GWAS P-value for that SNP.phenotype.qtl2: Name or ID of the second molecular phenotype (e.g., junction or editing-site).QTL_SNP.qtl2: Lead SNP for phenotype 2.QTL_P.qtl2: Association P-value for phenotype 2.QTL_Beta.qtl2: Effect size (β) of the lead SNP on phenotype 2.QTL_SE.qtl2: Standard error of the effect size for phenotype 2.QTL_MAF.qtl2: Minor allele frequency of the lead SNP for phenotype 2.QTL_chr.qtl2: Chromosome of the lead SNP for phenotype 2.QTL_pos.qtl2: Genomic position (bp, hg38) of the lead SNP for phenotype 2.GWAS_SNP_Beta.qtl2: GWAS beta for the same SNP in phenotype 2 context.GWAS_SNP_SE.qtl2: Standard error of GWAS beta for phenotype 2.GWAS_SNP_P.qtl2: GWAS P-value for phenotype 2 SNP.gene: Gene symbol or ID corresponding to the locus tested.nsnps: Number of SNPs included in the colocalization window.PP.H0.abf: Posterior probability that neither phenotype has a causal variant (no association).PP.H1.abf: Probability that only phenotype 1 has a causal variant.PP.H2.abf: Probability that only phenotype 2 has a causal variant.PP.H3.abf: Probability that both phenotypes have causal variants but they are independent.PP.H4.abf: Probability that both phenotypes share the same causal variant (colocalization).comparison: Indicates which QTL types were compared (e.g., sQTL vs eQTL, eQTL vs edQTL or sQTL vs edQTL).SNP_distance: Distance (bp) between the two lead SNPs for the compared QTLs.FDR.qtl1: FDR-adjusted significance for QTL1.FDR.qtl2: FDR-adjusted significance for QTL2.gene_name: Readable gene symbol.ed_region: Functional region annotation (e.g., intronic, exonic, CDS, intergenic).PP.H4: Simplified column for posterior probability of a shared signal (same as PP.H4.abf).PP.H3: Simplified column for posterior probability of independent signals (same as PP.H3.abf).TraitSpecific: Indicates which trait (QTL1 or QTL2) is trait-specific when PP.H1 or PP.H2 dominates.total: Total number of tests or summary metric per gene (if aggregated).category: Classification of the locus based on COLOC outcome (Ambiguous, Colocalized,  Independent or Trait-specific).

Preprints:

https://www.medrxiv.org/content/10.1101/2025.09.30.25337026v1,        https://www.medrxiv.org/content/10.1101/2025.09.25.25336663v1