significance threshold in alcohol and smoking GWAS analysis, we tested the polygenicity of alcoholism and smoking by exploring the overenrichment in variants that passed nominal threshold of significance in these datasets. The enrichment analysis was focused on eQTLs for the genes within modules that were correlated with AD in the module-trait correlation analysis. The two modules (thistle and brown4) that showed significant enrichment (p ≤ 0.05) in the Fisher exact test were subjected to 100,000 permutations to report the final P value of enrichment. We also performed the gene-based analysis by Multi-marker Analysis of GenoMic Annotation (MAGMA)26 on summary statistics of PGC-AD, UKBB-AC and TAG-CPD GWAS using Functional Mapping and Annotation of GWAS (FUMA-GWAS)27. The summary statistics of this gene-based analysis were overlaid on the IPA networks to identify the genes in these networks that also have nominal to moderate evidence of genetic contributions.
