We observed 1,306 CNVs (out of the 3,432 CNVs included in the WTCCC study) containing at least one SNP eQTL. Notably, CNVs that harbor a greater number of SNP eQTLs tend to be less well-tagged; this observation holds robustly after accounting for CNV minor allele frequency, which shows little correlation with the number of SNP eQTLs within the CNV (corr = 0.005). In particular, of the top 100 WTCCC CNVs ranked according to the number of SNP eQTLs within, only 31 are well-tagged (r2≥0.80) and 56 are tagged at r2<0.30.
