Mendelian Randomization results from GeneAtlas.

Table of the all significant (FDR 20]. pQTL for both cohorts are included, however, in order to avoid a ‘winner’s curse’, MR was conducted using data from the secondary protein cohort (ORCADES). Columns are ‘hgnc_symbol’: HUGO Gene Nomenclature Committee symbol of the exposure protein; ‘outcome_description’: description of the UK biobank outcome from GeneAtlas; ‘rsid’: rsID; ‘snpid’: ‘chr’_‘pos’; ‘chr’: chromosome (GRCh37); ‘pos’: position (GRCh37); ‘a1’: effect allele; ‘a0’: other allele; ‘exposure’: UniProtID of the protein; ‘ensembl_gene_id’: Ensembl (GRCh37) gene ID of the exposure protein; ‘n_exposure_pri’: number of individuals in the primary protein cohort (CROATIA-Vis); ‘freq1_exposure_pri’: frequency of the effect allele in the primary protein cohort (CROATIA-Vis); ‘beta1_exposure_pri’: regression coefficient (per additional effect allele) in the primary protein cohort (CROATIA-Vis); ‘se_exposure_pri’: standard error of ‘beta1_exposure_pri’; ‘p_exposure_pri’: p-value of ‘beta1_exposure_pri’ and ‘se_exposure_pri’; ‘info_exposure_pri’: SNPTEST (v2) imputation info score in the primary protein cohort (CROATIA-Vis); ‘n_exposure_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘freq1_exposure_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘beta1_exposure_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘se_exposure_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘p_exposure_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘info_exposure_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘outcome’: outcome code of the UK biobank outcome from GeneAtlas; ‘beta1_outcome’: beta of the effect allele on the outcome in GeneAtlas; ‘se_outcome’: standard error of ‘beta1_outcome’; ‘p_outcome’: p-value corresponding to ‘beta1_outcome’ and ‘se_outcome’; ‘info_outcome’: imputation info score in UK Biobank; ‘freq1_outcome’: frequency of the effect allele in UK Biobank; ‘beta_mr_delta_sec’: beta value using the delta MR method (using up to second order partial derivatives; See the appendix of Lynch and Walsh for further information) using estimates from the secondary cohort; ‘se_mr_delta_sec’: standard error of ‘beta_mr_delta_sec’ using the delta MR method (using up to first order partial derivatives; See the appendix of Lynch and Walsh for further information) using estimates from the secondary cohort; ‘p_mr_delta_sec’: p-value corresponding to ‘beta_mr_delta_sec’ and ‘se_mr_delta_sec’; ‘fdr_sig_mr_delta_sec’: significance of ‘p_mr_delta_sec’ at a False Discovery Rate (FDR) of (TSV)