SNP and SNP-set results for high-density lipoprotein (HDL) cholesterol in the heterogenous stock of mice from the Wellcome Trust Centre for Human Genetics.

We analyze J ≈ 10,000 SNPs and G = 1, 925 SNP-sets from N = 1,814 mice—with specific numbers varying slightly depending on the quality control procedure for each phenotype (Supporting information). Here, SNP-set annotations are based on gene boundaries defined by the Mouse Genome Informatics database (see URLs listed in the main text). Unannotated SNPs located within the same genomic region were labeled as being within the “intergenic region” between two genes. This file gives the posterior inclusion probabilities (PIPs) for the input and hidden layer neural network weights after fitting the BANNs model on the individual-level data. We assess significance for both SNPs and SNP-sets according to the “median probability model” threshold [57] (i.e., PIP ≥ 0.5). Page #1 provides the variant-level association mapping results with columns corresponding to: (1) chromosome; (2) SNP ID; (3) chromosomal position in base-pair (bp) coordinates; (4) SNP PIP; and (5) SuSiE PIP, which corresponds to SNP-level posterior inclusion probabilities computed by SuSiE [46]. Page #2 provides the SNP-set level enrichment results with columns corresponding to: (1) chromosome; (2) SNP-set ID; (3-4) the starting and ending position of the SNP-set chromosomal boundaries; (5) SNP-set PIP; (6) RSS PIP, which corresponds to the posterior inclusion probabilities computed by RSS [26]; (7) the number of SNPs that have been annotated within each SNP-set; (8) the “top” associated SNP within each SNP-set; (9) the PIP of each top SNP. (XLSX)