Fig. 4. Inferred skeletons that represent associations that are robust to conditioning.

a The skeleton inferred among the phenotypes (G_T). The edges represent phenotype pairs that remain associated at p₁ < 1 × 10⁻⁷ when conditioned on other phenotypes. In this computation for a pair of variables X and Y, we tested the association between X and Y conditioning on all other phenotypes or all other phenotype pairs. Arrows point out to clusters detected with MCODE. b The effect of conditional independence filtering on genome-wide association analysis (GWAS) results. Here we show the effect of removing variant–phenotype pairs (detected in a standard GWAS) for which there exists another phenotype whom conditioning upon renders the association insignificant (>p₂).