This README accompanies the files with eQTS results from eQTLGen File with full eQTS results: 2019-12-12-eQTSFDR-CohortInfoRemoved-BonferroniAdded.txt.gz File with significant (FDR<0.05) eQTS results: 2019-12-12-eQTSFDR0.05-CohortInfoRemoved-BonferroniAdded.txt.gz 2019-12-12-eQTSFDR-CohortInfoRemoved-BonferroniAdded.txt.gz =========================================================== Column Names ------------ Pvalue - P-value Trait - Unique ID for trait, including pubmed ID and GWAS P-value used for calculating PGS Zscore - Z-score (corresponding to higher PGS) Gene - ENSG name (Ensemblv71) of the eQTL gene GeneSymbol - HGNC name of the gene GeneChr - Gene chromosome GenePos - Centre of gene position NrCohorts - Total number of cohorts where this genetic risk score-gene combination was tested NrSamples - Total number of samples where this genetic risk score-gene combination was tested FDR - False discovery rate estimated based on permutations BonferroniP - P-value after Bonferroni correction 2019-12-12-eQTSFDR0.05-CohortInfoRemoved-BonferroniAdded.txt.gz =============================================================== Column Names ------------ Pvalue - P-value PGS - Unique ID for trait including pubmed ID Trait - Trait for which the polygenic score was calculated PGS_Pvalue - GWAS P-value threshold used to calculate the PGS PubmedID - Pubmed ID of corresponding GWAS Zscore - Z-score Gene - ENSG name (Ensemblv71) of the eQTL gene GeneSymbol - HGNC name of the gene GeneChr - Gene chromosome GenePos - Centre of gene position NrCohorts - Total number of cohorts where this genetic risk score-gene combination was tested NrSamples - Total number of samples where this genetic risk score-gene combination was tested FDR - False discovery rate estimated based on permutations Additional information ---------------------- These files contain all eQTS results from eQTLGen, accompanying the article. 19,942 genes that showed any expression in blood were tested. 1,263 GWAS summary statistics were curated, used to calculate polygenic scores, and tested for association with gene expression. FDR calculation --------------- To determine nominal P-value threshold corresponding to FDR=0.05, we used a "pruned" set of traits to perform permutation-based FDR calculation (see Methods). Updates ------- 2019-12-12 We have updated the eQTS files: The previous version had the sign of all results swapped, this is now fixed (i.e. the Z-score is now relative to a polygenic score increasing a trait) The current version includes Bonferroni-adjusted p-values