This README accompanies the files with cis-eQTL, trans-eQTL and eQTS replication results: Cis-eQTL replication results in GTEx v7 ======================================= File name: 2019-12-11-cisEQTL-ReplicationOfTopEffectsInGTEx_WoGTEx_TwoCohortFix.txt.gz Column Names ------------ First row: denotes dataset names First is eQTLGen discovery analysis and following indicate datasets where replication analyses were performed. Second row: Gene - ENSG name (Ensembl v71) of the eQTL gene Gene-Chr - Gene chromosome Gene-Pos - Centre of gene (hg19) RsId - SNP rs ID SNP-Chr - SNP chromosome SNP-Pos - SNP position (hg19) Alleles - SNP alleles AlleleAssessed - Assessed allele, the Z-scores refers to this allele Z - Z-score (FROM THE FIRST DATASET) Rsq - R-squared (FROM THE FIRST DATASET) P - P-value (FROM THE FIRST DATASET) Significant - Is the replication significant (FDR<0.05 and same allelic direction, true/false) (FROM THE FIRST DATASET). ... Additional information ---------------------- Separate discovery analysis was conducted, by excluding GTEx whole blood. Top effects (strongest eQTL effect per gene) were replicated for 16,963 cis-eQTL genes in GTEx v7 datasets https://gtexportal.org/. Trans-eQTL replication results in GTEx post-mortem tissues ========================================================== File name: 2020-11-17-transEQTL-Replication-MasterTable-GTEx.txt.gz Column Names ------------ First row denotes dataset names. The first columns describe the eQTLGen discovery analysis results without the GTEx whole blood dataset. The following columns indicate the GTEx tissues where replication analyses were performed. Second row: Gene - ENSG name (Ensembl v71) of the eQTL gene Gene-Chr - Gene chromosome Gene-Pos - Centre of gene (hg19) RsId - SNP rs ID SNP-Chr - SNP chromosome SNP-Pos - SNP position (hg19) Alleles - SNP alleles AlleleAssessed - Assessed allele, the Z-scores refers to this allele Z - Z-score (FROM THE FIRST DATASET) Rsq - R-squared (FROM THE FIRST DATASET) P(differentEffectSize) - P-value denoting the difference of the effect sizes compared to eQTLGen discovery analysis (FROM THE FIRST DATASET) P - P-value (FROM THE FIRST DATASET) FDR - Benjamini-Hochberg FDR (FROM THE FIRST DATASET). ... Additional information ---------------------- Separate discovery analysis was conducted while excluding GTEx whole blood dataset and first columns shows results reaching FDR<0.05 in this separate discovery analysis. Trans-eQTL replication results in single cell RNA-seq datasets ============================================================== File name: 2020-11-11_eQTLGen_trans-eQTLs_single-cell_replications_missingness_filter_Z_p_AF_b_se.txt.gz Column Names ------------ First row denotes dataset names. First is eQTLGen discovery analysis and following indicate single cell RNA-seq eQTL datasets where replication analyses were performed. Second row: SNP - SNP rs ID SNPChr - SNP chromosome SNPPos - SNP position (hg19) Gene - ENSG name (Ensembl v71) of the eQTL gene GeneSymbol - HGNC gene name of the eQTL gene GeneChr - Gene chromosome GenePos - Centre of gene (hg19) NrSamples - Number of samples where the eQTL was tested in eQTLGen AssessedAllele - Assessed allele, the Z-scores refers to this allele OtherAllele - Not assessed allele eQTLGen_AssessedAlleleFrequency - Allele frequency of the SNP in eQTLGen (refers to Assessed Allele) Zscore - Z-score in eQTLGen Pvalue - P-value in eQTLGen Beta - Beta in eQTLGen SE - Standard error in eQTLGen replication_AssessedAllele - Assessed allele from the single cell replication replication_AssessedAlleleFrequency - Allele frequency of the SNP in single cell datasets (refers to replication_AssessedAllele) _Zscore - Z-score in replication cell type _Pval - P-value in replication cell type _beta - Beta in replication cell type _SE - Standard error in replication cell type Additional information --------------------- Beta and SE were estimated by formula as provided by Zhu et al 2016 (https://www.nature.com/articles/ng.3538; Supplementary Information). We did not provide this file with initial submission. Trans-eQTL replication results in purified cell types, cell lines and methylation datasets ========================================================================================== File name: 2020-11-17-transEQTL-Replication-MasterTable-nonGTEx.txt.gz Column Names ------------ First row denotes dataset names. The first columns describe the eQTLGen discovery analysis results. The second and third datasets are analyses done in size-matched whole blood and PBMC subsets of eQTLGen discovery analysis. These are not replications. The following columns indicate datasets where replication analyses were performed: CD4, CD8, CD14, CD15, CD19, Macrophage, Platelet purified cell types, iPSCs, LCLs and Methylation. Methylation data from BIOS has sample overlap with discovery analysis and should not be considered as independent replication. Second row: Gene - ENSG name (Ensembl v71) of the eQTL gene Gene-Chr - Gene chromosome Gene-Pos - Centre of gene position (hg19) RsId - SNP rs ID SNP-Chr - SNPChr SNP-Pos - SNPPos (hg19) Alleles - SNP alleles AlleleAssessed - Assessed allele, the Z-scores refers to this allele Z - Z-score (FROM THE FIRST DATASET) Rsq - R-squared (FROM THE FIRST DATASET) P(differentEffectSize) - P-value denoting the difference of the effect sizes compared to eQTLGen discovery analysis (FROM THE FIRST DATASET) P - P-value (FROM THE FIRST DATASET) FDR - Benjamini-Hochberg FDR (FROM THE FIRST DATASET). ... Additional information ---------------------- Methylation has sample overlap with discovery analysis (BIOS samples) and should not be considered as independent replication. Rather it indicates whether trans effects on gene expression are showing QTL effects on different data modality (methylation). This freeze includes a new version of iPSC replication and is now separate from the GTEx replication. eQTS replication results in GTEx tissues (EUR subset of samples) ================================================================ File name: 2020-11-17-eQTS-Replication-MasterTable-GTEx.txt.gz Column Names ------------ First row denotes dataset names. The first columns describe the eQTLGen discovery analysis results without the GTEx whole blood dataset. The following columns indicate the GTEx tissues where replication analyses were performed. Second row: Gene - ENSG name (Ensembl v71) of the eQTL gene Gene-Chr - Gene chromosome Gene-Pos - Centre of gene (hg19) RsId - Polygenic risk score (naming is ___) SNP-Chr - N/A SNP-Pos - N/A Alleles - SNP alleles (we used 'C/T' for all risk scores) AlleleAssessed - Assessed allele, the Z-scores refers to this allele. The 'C' allele corresponds to the trait-increasing polygenic score. Z - Z-score (FROM THE FIRST DATASET) Rsq - R-squared (FROM THE FIRST DATASET) P(differentEffectSize) - P-value denoting the difference of the effect sizes compared to eQTLGen discovery analysis (FROM THE FIRST DATASET) P - P-value (FROM THE FIRST DATASET) FDR - Benjamini-Hochberg FDR (FROM THE FIRST DATASET). ... Additional information ---------------------- Separate discovery analysis was conducted while excluding GTEx whole blood dataset and first columns shows results reaching FDR<0.05 in this separate discovery analysis. Because GWASs used for calculating polygenic risk scores originated primarily from European cohorts, we used European subset of GTEx samples for eQTS replication. In our analyses, polygenic scores were coded to dummy C/T SNPs where C corresponds to higher polygenic score and T corresponds to lower polygenic score. We did not provide this file with initial submission. eQTS replication results cell lines ========================================== File name: 2020-11-17-eQTS-Replication-MasterTable-nonGTEx.txt.gz Column Names ------------ First row denotes dataset names. The first columns describe the eQTLGen discovery analysis results. The second and third datasets are analyses done in size-matched whole blood and PBMC subsets of eQTLGen discovery analysis. These are not replications. The following columns indicate datasets where replication analyses were performed: iPSCs, LCLs. Second row: Gene - ENSG name (Ensembl v71) of the eQTL gene Gene-Chr - Gene chromosome Gene-Pos - Centre of gene (hg19) RsId - Polygenic risk score (naming is ___) SNP-Chr - N/A SNP-Pos - N/A Alleles - SNP alleles (we used 'C/T' for all risk scores) AlleleAssessed - Assessed allele, the Z-scores refers to this allele. The 'C' allele corresponds to the trait-increasing polygenic risk score. Z - Z-score (FROM THE FIRST DATASET) Rsq - R-squared (FROM THE FIRST DATASET) P(differentEffectSize) - P-value denoting the difference of the effect sizes compared to eQTLGen discovery analysis (FROM THE FIRST DATASET) P - P-value (FROM THE FIRST DATASET) FDR - Benjamini-Hochberg FDR (FROM THE FIRST DATASET). ... Additional information ---------------------- In our analyses, polygenic scores were coded to dummy C/T SNPs where C corresponds to higher polygenic score and T corresponds to lower polygenic score. This freeze includes a new version of iPSC replication and is now separate from the GTEx replication.