< 0.6, with MAF < 1% or with estimated odds ratio > 25 or smaller than 1/25, as well as SNPs located in the MHC region (chr6:25–34 Mb). We set a window of 35 kb upstream to 10 kb downstream of the gene coordinates to compute gene-level association statistics and used the European reference panel from the phase 3 of the 1000 Genomes Project as the reference population113. We then used MAGMA to test whether the 10% most specific genes (with an expression of at least 1 TPM or 1 UMI per million) for each cell type/tissue were associated with BD. The P-value threshold for significance was P < 9.1 × 10−3, representing a 5% false discovery rate (FDR) across datasets.
