Additional file 1 of A comprehensive study of genetic regulation and disease associations of plasma circulatory microRNAs using population-level data

Additional file 1: Table S1. The list of 2,083 miRNAs characterised in this study (including 591 were well-expressed). Table S2. Baseline characteristics of study participants. Table S3. Genome-wide significant miR-eQTLs identified in this study. Table S4. miR-eQTLs explaining high proportion of variation in miRNA level. Table S5. Multi-SNP joint analysis for conditionally independent associations from GCTA-COJO. Table S6. Replicated miR-eQTLs in Nikpay et al. Table S7. Summary of replication of miR-eQTLs. Table S8. List of 4,310 replicated miR-eQTLs. Table S9. Functional annotation of miR-eQTLs. Table S10. List of 22 loci, miRNAs, and corresponding genes, and 19 loci harbored miRNAs with replicated miR-eQTLs across cohorts. Table S11. SNPs in miRNA genes that also affected miRNA levels. Table S12. miR-eQTLs located in the promoter region of miRNAs. Table S13. SNP-based heritability estimates for 2,083 miRNAs. Table S14. Overlap between cis-miR-eQTLs and gene expression QTLs (eQTLs). Table S15. Colocalisation analysis between plasma miRNAs and gene expression in whole blood (eQTLGen) and across tissues (GTEx). Table S16. miRNAs with shared eQTLs with their putative target genes. Table S17. Overlap and colocalisation analysis between cis-miR-eQTLs and pQTLs. Table S18. Overlap between trans-miR-eQTLs and pQTLs. Table S19. Overlap between trans-miR-eQTLs and pQTLs in Olink. Table S20. Overlap of miR-eQTLs, met-QTLs, linear regression, and colocalisation analysis. Table S21. GWAS traits associated with miR-eQTLs. Table S22. Association between miR-eQTLs in locus in chr9:136128546-136296530 and other omics/phenotypes. Table S23. Genetic instruments for miRNAs (FDR<0.1) for PheWAS and MR analysis. Table S24. FDR-significant association for PheWAS using single variant and cis-GRS. Table S25. Cis and extended-GRS for 17 significant associations in MR-PheWAS. Table S26. Full results for cis-MR analyses. Table S27. Full results for extended-MR analyses. Table S28. Full results for replication using large GWAS summary statistics. Table S29. Reverse-MR to test association between obesity-related traits and miR-543 and miR-329-3p. Table S30. Target genes of miR-543 and miR-329-3p associated with BMI or WHR. Table S31. Univariable MR analysis on the associations between miR-1908-5p and metabolites (Metabolon platform). Table S32. Univariable MR analysis on the associations between 12 candidate metabolites and the risk of benign neoplasm of colon. Table S33. MR-Bayesian Model Averaging to identify most likely causal metabolites using a range of prior probabilities. Table S34. Mediation analysis to quantify the proportion of miR-1908-5p on the risk of benign neoplasm of colon mediated by 1-palmitoyl-2-linoleoyl-GPE. Table S35. Multivariable MR between miR-1908-5p and candidate metabolites on benign neoplasm of colon.