We observed a paucity of autosomal CNVs overlapping RefSeq genes, compared to random permutations (Supplementary Fig. 1.2). This impoverishment is more strongly associated with deletions than duplications or multiallelic loci (Fig. 2a), and in common CNVs (minor allele frequency (MAF) > 10%) compared to rare CNVs (MAF < 1%) (Fig. 2b). The bias of common deletions away from genes is stronger in YRI than in CEU (Fig. 2b), which is also consistent with weaker selection against deleterious base substitutions in CEU than YRI22. There was also a bias of CNVs away from enhancers and ultra-conserved elements, but not from promoters or DNaseI hypersensitive sites (Supplementary Fig. 1.2). Indeed duplications seem to be significantly enriched among promoters and stop codons, perhaps corroborating a previous observation of indel enrichment at either end of genes23.
