How can we use this to understand disease?

Let's look at coronary heart disease.

CNNs can predict and interpret effects of disease-associated genetic variants in the relevant tissue context.

We look at unstimulated coronary smooth muscle cells. Genome-wide association study says a certain C->T variant is super important. However, the neural network indicates it doesn't matter.

When we stimulate these cells, the neural network actually finds a certain word - that has the position of the C - that is important.

So we find that stimulated cells are the ones that are important to target, not unstimulated cells.