New technologies have allowed us to collect genetic data on many thousands of individuals. The primary purpose of these data is to look for correlations between genetic markers and common diseases such as diabetes. This has been a very successful approach for common diseases. Now we would like to push these data further to compare and contrast the genetic variants we’ve identified and how they relate to one another. Identifying the genetic variants that are shared between diseases and those that are distinct can give further insights into the mechanisms of disease. We hope that these clues can be used to improve the prediction, prevention and treatment of disease.