Fig. 2

Distributions of single-SNP and haplotype tests. A, B Null (gray line) and alternative (black line) distributions of Bayes factors for single SNP and haplotype and their Manhattan plots. Log₁₀BF values under alternative distributions truncated at 10; null distribution obtained by permuting the phenotype once. Alternative distributions obtained using true phenotype. C Functional analysis of involved genes in (A) with > 6 log₁₀BF (n = 17). Upper image shows significantly enriched GO terms (FDR < 0.05); biological processes mainly involved three genes: HLA-H, HLA-DPB1, and HLA-DPA1. Lower image shows distribution of involved KEGG pathways for involved genes. D Examples of genome-wide significant haplotype associations. LD block (based on local haplotype sharing) around each significant marker of same region (red “+”) denoted with gray shaded line. Genes of interest within LD block shown as solid segments