Manhattan plots of variant-level fine mapping results for six traits in heterogenous stock of mice from the Wellcome Trust Centre for Human Genetics.

Traits are grouped based on their category and include: (A) body mass index (BMI) and body weight, (B) percentage of CD8+ cells and mean corpuscular hemoglobin (MCH), and (C) high-density and low-density lipoprotein (HDL and LDL, respectively) cholesterol. Posterior inclusion probabilities (PIP) for the input layer 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 (MPM)” threshold [57]. Here, we only color code SNPs that had a PIP greater than 1% in either trait. SNPs with PIPs exceeding 1% in both traits are marked by a star and denoted as falling in the “overlap” category. BANNs estimated the following PVEs on the SNP and SNP-set levels for these traits, respectively: (i) 0.09 and 0.08 for BMI, (ii) 0.39 and 0.40 for body weight, (iii) 0.51 and 0.48 for percentage of CD8+ cells, (iv) 0.34 and 0.32 for MCH, (v) 0.34 and 0.28 for HDL, and (vi) 0.15 and 0.15 for LDL. (PDF)