Mendelian Randomization results from studies identified using Phenoscanner.

Table of all Mendelian Randomization results using data acquired through Phenoscanner [21,22]. 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. Columns are ‘hgnc_symbol’: HUGO Gene Nomenclature Committee symbol of the exposure protein; ‘trait’: outcome trait description; ‘snp’: chr‘chr’:‘pos’; ‘rsid’: rsID; ‘chr’: chromosome (GRCh37); ‘pos’: position (GRCh37); ‘a1’: effect allele; ‘a0’: other allele; ‘exposure’: UniProtID of the 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; ‘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); ‘ensembl_gene_id’: Ensembl (GRCh37) gene ID of the exposure protein; ‘study’: name of the consortium/lead author of the outcome study; ‘pmid’: PubMed ID of the outcome study; ‘ancestry’: ancestry of the population within which the outcome was measured; ‘year’: the year the outcome study was published; ‘beta1_outcome’: regression coefficient (per additional effect allele) in the outcome study; ‘se_outcome’: standard error of ‘beta1_outcome’; ‘p_outcome’: p-value of ‘beta1_outcome’ and ‘se_outcome’; ‘n_outcome’: number of individuals in the outcome study; ‘n_cases_outcome’: number of cases in the outcome study; ‘n_controls_outcome’: number of controls in the outcome study; ‘n_studies_meta_outcome’: if a meta-analysis, number of studies included; ‘units_outcome’: units of analysis in the outcome study (IVNT stands for inverse normal rank transformed phenotype); ‘dataset’: Phenoscanner dataset ID; ‘beta1_outcome_flipped’: has the sign of ‘beta1_outcome’ been inverted from that provided by Phenoscanner due to calling of the effect vs. non-effect allele? True / False; ‘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 <5% (True / False).
(TSV)