Colocalization analysis using JLIM and Coloc

We selected 1,621 PU.1-trait pairs at loci where the significant PU.1 bQTLs also show at least one blood cell trait association at p < 10⁻⁶ to perform colocalization. For JLIM,^23,90 we used the default parameters. p values were derived by permuting the PU.1 binding level matrix. For Coloc,²² we used the prior parameters p₁ = 10⁻⁴, p₂ = 10⁻⁴, and p₁₂ = 10⁻⁶, which is more conservative than the default, and ran Coloc on the summary statistics. For both analyses, we considered variants within a 200-kb window around the GWAS lead variant. We used a significance threshold of p < 0.01172 (FDR <5%) for JLIM and posterior probability of colocalization (PP(Colocalization)) > 0.5. The FDR cutoff for JLIM was determined by the equation:

where p_cutoff is the p value cutoff, N is the number of PU.1-trait loci tested, and P_JLIM is the JLIM p value.