Additional file 1 of Multi-trait association studies discover pleiotropic loci between Alzheimer’s disease and cardiometabolic traits

Additional file 1: Supplemental Methods – Details on how we collected the GWAS summary statistics and how the statistical analyses were performed. Figure S1. ADAM10 locus – LocusZoom plots of the pleiotropic signals and the MINDY2 eQTL signal at the ADAM10 locus. Figure S2. ADAMTS4 locus – LocusZoom plots of the pleiotropic signals and NDUFS2 eQTL signal at the ADAMTS4 locus. Figure S3. T2D at ACE locus – LocusZoom plots of the T2D signals at the ACE locus. Figure S4. DOC2A locus – LocusZoom plots of the pleiotropic signals and FAM57B and DOC2A eQTL signal at the DOC2A locus. Figure S5. SPPL2A locus – LocusZoom plots of the pleiotropic signals and SPPL2A eQTL signal at the SPPL2A locus. Figure S6. CCNT2 locus – LocusZoom plots of the pleiotropic signals and CCNT2 eQTL signal at the CCNT2 locus. Supplementary Table 1. Bivariate normal estimates for the SNP Z-scores of each bivariate GWAS. Supplementary Table 2. Number of SNPs that passed each filter for the AD-centric analysis. Supplementary Table 3. Number of SNPs that passed each filter for the locus discovery analysis. Supplementary Table 4. Single-tissue eQTLs for rs4308 downloaded from GTExPortal. Supplementary Table 5. Single-tissue eQTLs for rs442495 downloaded from GTExPortal. Supplementary Table 6. Single-tissue eQTLs for rs4575098 downloaded from GTExPortal. Supplementary Table 7. Single-tissue eQTLs for rs10496731 downloaded from GTExPortal. Supplementary Table 9. Single-tissue eQTLs for rs12595082 downloaded from GTExPortal. Supplementary Table 10. List of approximate conditional analyses. Supplementary Table 11. AD-centric bivariate analysis single-tissue-eQTL results. Supplemental Table 13. Human Splice Finder 3 results for rs144867634. Supplemental Table 14. AVISPA results on rs144867634 A allele. Supplemental Table 15. AVISPA results on rs144867634 G allele.