List of pQTLs (linkage disequilibrium clumped).

List of lead SNPs for each protein following linkage disequilibrium (LD) clumping, together with replication information. Biallelic variants within ±5Mb and r2 >0.2 to the lead variant (smallest p-value at the locus) were clumped together. European populations in 1,000 Genomes [71,72] were used as the LD reference. Columns are: ‘hgnc_symbol’: HUGO gene naming consortium symbol of the exposure (protein); ‘snpid’: ‘chr’_‘pos’; ‘rsid’: rsID; ‘chr’: chromosome (GRCh37) of the SNP; ‘pos’: position (GRCh37) of the SNP; ‘a1’: effect allele; ‘a0’: other allele; ‘n_pri’: number of individuals in the primary cohort (CROATIA-Vis); ‘freq1_pri’: frequency of the effect allele in the primary cohort (CROATIA-Vis); ‘beta1_pri’: beta estimate of the effect allele in the primary cohort (CROATIA-Vis); ‘se_pri’: standard error of ‘beta1_pri‘ in the primary cohort (CROATIA-Vis); ‘p_pri’: p-value of ‘beta1_pri‘ and ‘se_pri’; ‘info_pri’: SNPTEST (v2) info of the imputation in the primary cohort (CROATIA-Vis); ‘r2_pri’: coefficient of determination of the regression in the primary cohort (CROATIA-Vis); ‘n_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘freq1_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘beta1_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘se_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘p_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘info_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘r2_sec’: as for the primary cohort (CROATIA-Vis) but in the secondary cohort (ORCADES); ‘uniprot_swissprot’: UniProtID of the exposure (protein), see http://www.uniprot.org/; ‘ensembl_gene_id’: Ensembl gene ID (GRCh37; see http://grch37.ensembl.org/index.html) of the gene-of-origin of the protein; ‘chromosome_name’: chromosome (GRCh37) of the gene of the protein, as per Ensembl GRCh37; ‘start_position’: start position (GRCh37) of the gene of the protein, as per Ensembl GRCh37; ‘end_position’: end position (GRCh37) of the gene of the protein, as per Ensembl GRCh37; ‘description’: HUGO gene naming consortium description of the exposure (protein); ‘replicated_pqtl’: is the lead SNP of the cluster (as identified in the primary cohort) replicated in the secondary cohort (Bonferroni correction for multiple testing. TRUE if it is; FALSE if not); ‘within_gene_plus_flank_tol’: is the SNP within the gene-of-origin of the protein +/- 150kb (TRUE is it is; FALSE if not).
(TSV)