to say about low frequency variants. Despite these current limitations, the annotation system we implemented in SCAN should prove useful to other investigators and seeks to be as comprehensive as possible by providing functional information for the most extensive map of CNVs to date from the recent population-based genome-wide survey [7]. Since the MAF spectrum of the NHGRI catalog of trait-associated SNPs from published GWAS is quite different from that of the SNPs on the genotyping platforms used to conduct these GWAS, we performed our enrichment analyses while conditioning on the MAF distribution. There are other potential representational biases in the NHGRI catalog of reported variants that may have affected our studies. The enrichment in disease classes relative to other classes of traits, for example, may be the result of increased power (e.g., due to greater sample sizes) for these categories.
