Results of secondary analyses of discovery GWAS data are shown in Supplementary Table S3 (gene-based analyses), Supplementary Figure S6 and Supplementary Table S4 (network analyses) and Supplementary Table S5 (geneset analyses). Gene-based analyses assess over-representation of case-control allele frequency differences in all SNPs within defined genic regions (with LD pruning or weighting as described in Supplementary Materials and Methods). The hybrid set-based test (HYST) incorporated in KGG shows strong gene-based association of AD with COL6A3 (p=7.30×10−9, q=0.00016), RYR3 (p=2.62×10−7, q=0.0029) and LOC339975 (p=5.31×10−6, q=0.0248) (Supplementary Table S3).
