Supplementary Figures

Each notebook is fully executable and documented to ensure reproducibility of our results. The main sections include:

• Figure S2: Extended performance comparison of ColocBoost against other multi-trait colocalization methods.

• Figure S3: Additional metrics to benchmark performance of ColocBoost with other multi-trait colocalization methods.

• Figure S4: Hyperparameter sensitivity and robustness analysis for ColocBoost.

• Figure S5: Extended ColocBoost xQTL analysis in aging human brain.

• Figure S6: Functional enrichment of colocalized variants.

• Figure S7: Properties of genes with multiple causal variants.

• Figure S8: xQTL-only ColocBoost for eQTLs across 13 brain tissues in GTEx.

• Figure S9: Validation of ColocBoost colocalization.

• Figure S10: Extended disease heritability analyses of variant-level functional annotations derived from ColocBoost.

• Figure S11: Extended evaluations of GWAS-xQTL colocalization from ColocBoost and competing methods.

• Figure S12: Additional summary of genome-wide GWAS-xQTL colocalization results.

• Figure S13: Example cases of xQTL colocalizations in known AD risk genes.

• Figure S14: Additional details of colocalizations in gene CTSH.