Manhattan plot of variant-level association mapping results for high-density and low-density lipoprotein (HDL and LDL, respectively) traits in ten thousand randomly sampled individuals of European ancestry from the UK Biobank [31].

Posterior inclusion probabilities (PIP) for the neural network weights are derived from the BANNs model fit on individual-level data and are plotted for each SNP against their genomic positions. Chromosomes are shown in alternating colors for clarity. The black dashed line is marked at 0.5 and represents the “median probability model” threshold [57]. SNPs with PIPs above that threshold are color coded based on their SNP-set annotation. Here, SNP-set annotations are based on gene boundaries defined by the NCBI’s RefSeq database in the UCSC Genome Browser [50]. Unannotated SNPs located within the same genomic region were labeled as being within the “intergenic region” between two genes. These regions are labeled as Gene1-Gene2 in the legend. Gene set enrichment analyses for these SNP-sets can be found in S31 Fig. Stars (★) denote SNPs and SNP-sets that replicate findings from our analyses of HDL and LDL in the Framingham Heart Study (see Fig 4 in the main text). (PDF)