Fig. 2

The ranking, model fitting and explanation phases. In the ranking phase, the SNPs and environmental features are ordered by their relative importance. The ranking is achieved with XGBoost and SHAP values as explained in Fig. 4. In the model fitting process, the top ranked features are combined and modelled with XGBoost as described in Fig. 6. Finally, the explanations and interactions are obtained from the SHAP values. This is visualized in Figs. 10, and 11