Access to the deep whole genome sequences of 69 individuals from Complete Genomics (Drmanac et al. 2010) allows us to investigate the average frequency of variants that intersect functional DNA elements. These genomes collectively contain 19,124,349 SNVs and 3,040,170 insertion/deletions. The average individual contains 3,870,827 variants, of which ∼56.23% fall within any of our annotations (excluding histones, which alone cover 99.5% of the SNVs, standard deviation = 0.005). This count is substantially higher than those SNVs that affect protein coding sequences alone (∼9%). As expected, variants intersect multiple regulatory annotations. An example is shown in Figure 1; this variant falls within several regulatory elements, resides in several genomes, and has been shown to directly affect binding of NFKB (Kasowski et al. 2010).
