Fig. 3

Manhattan plots and linkage disequilibrium (LD; \(R^2\)) heatmaps from the second-stage variant-level analysis of the HCHS/SOL data, using the PC-adjusted KRV. Each panel corresponds to a distinct gene or gene region. The Bray-Curtis kernel was used for analysis of variants in the IL23R-C1orf141 region; the unweighted UniFrac kernel was used for analysis of variants in ZFR and MTMR12. The top 5 PCs of genome-wide genetic variability were adjusted. The red lines represent variant-level significance after Bonferroni correction (\(\alpha = 8.98 \times 10^{-5}\) for variants in the IL23R-C1orf141 region, and \(1.08 \times 10^{-4}\) for variants in ZFR and MTMR12). A large \(R^2\) value indicates high LD