Additional file 3 of Genome-wide multi-trait analysis of irritable bowel syndrome and related mental conditions identifies 38 new independent variants

Additional file 3: Table S1. a Univariate and bivariate MiXeR output for IBS vs. neuroticism. Table S2. Results from association analyses of lead and secondary lead variants conditioned on the lead variant using COJO. For locus with more than two secondary variants, we further check independency of the secondary variants among each other. P-value of the secondary variants in MTAG-IBS and P-value after conditional analysis using COJO are given. The last column in the right indicates whether the secondary variant was considered as an independent signal. Table S3. Results in the original GWAS on IBS of the lead SNPs from MTAG-IBS. Table S4. Credible variants for each of the 37 independent loci or IBS identified in the cross-trait analysis using MTAG. Variants included herein were identified by all three fine-mapping methods (PAINTOR, CAVIARBF and FINEMAP). The prosterior probability of the variant being causal estimated by PAINTOR, CAVIARBF and FINEMAP is indicated in the last three columns. Chromosome (CHR), base position (BP), and SNP of the index variants. Effect alle (A1) and non-effect allele (A2) with respect to the beta (BETA). The standard error of the beta (SE) and the association P-value. Table S5. Functional annotation of the credible variants for each of the 42 lead variants identified in the cross-trait analysis of IBS using MTAG. Chromosome (CHR), SNP of the index variants, base position (BP), combined Annotation Dependent Depletion score (CADD), RegulomeDB score (RDB) and chromatin state (minChrState) are indicated. Table S6. GWAS Catalog results for MTAG-IBS credible set variants associated with other traits in previous GWAS. Table S7. Variants in credible sets mapped to genes associated with eQTLs. Table S8. Genes mapped to sets of crediable variants in FUMA. Table S9. Enrichment of genes mapped to variants in credible sets. Table S10. Results of the gene-based asociation analysis on MTAG-IBS using MAGMA. Only gene-wide signficant genes are shown. The p-value for gene-wide significance after Bonferroni correction was 0.05/18,135=2.757x10-6. Table S11. Results of the gene-set analysis on MTAG-IBS using MAGMA. Table S12. Enrichment analysis on druggable genes for MTAG-IBS genes using data from PharmaKG.Categories according to the Anatomical Therapeutic Chemical (ATC) classification system are provided. Table S13. Results of the partitioned heritability analysis using LDSC. Table S14. Genetic correlations between MTAG-IBS and 28 phenotypes inlcuding digestive, immnological and psychiatric disorders from MR-Base. Table S15. a CAUSE model comparison.