CNVs are disproportionately more likely to predict transcript levels than frequency-matched SNPs, and they are more likely to affect many different gene expression traits as master regulatory polymorphisms. An important issue to address is whether the enrichment of tCNVs as eQTLs and as disease-associated SNPs are correlated. Note that the probability that a random SNP is found in the NHGRI catalog increases from 0.062% in the set of HapMap SNPs to about 0.5% (more than 5-fold) in the set of well-tagged CNVs that are not eQTLs and to 2% in the tCNVs that are eQTLs.
