Hadn't heard of that before, thanks! In this case, I understood the question to be "will deep learning do a good job predicting the function of/phenotype emerg

Hadn't heard of that before, thanks! In this case, I understood the question to be "will deep learning do a good job predicting the function of/phenotype emerging from individual SNPs" and I don't think model interpretation would help (for starters, the model is trained to predict linkage and doesn't deal with data related to phenotypes).