The ENCODE project is still ongoing. Using saturation techniques, we believe we only have discovered a maximum 50% of elements. This number is likely to be lower due to inaccessible cell types and other factors. Also, several cell types are extremely rare and dicult to access, so sequencing data from these cell types is another challenge.
In computational frontiers, the ENCODE project has produced an enormous amount of raw data. Similar to how the full sequence of the human genome unleashed a series of computational projects, the ENCODE data can be used for a variety of computational projects.