Although the catalog of information is important, its interpretation is even more so. To assist comparison among annotations, we developed a heuristic scoring system based on functional confidence of a variant. The scoring system represents with increasing confidence that a variant lies in a functional location and likely results in a functional consequence (i.e., alteration of TF binding and a gene regulatory effect) (Table 2). As such, we consider variants that are known eQTLs for genes, and thus have been shown to be associated with expression, as most likely to be significant and label these variants as Category 1. However, 58% of eQTL SNVs are not associated with any other functional annotation and are labeled Category 6. Within Category 1, subcategories indicate additional annotations from the most confident (1a, which has TF binding, a motif for that TF, and a DNase footprint) to the least confident (1f, which has only TF binding or a DNase peak).
