Since the deletion/duplication of multiple regulatory SNPs may result in aberrant transcription or disease, we evaluated the presence of SNP eQTLs within CNVs. We identified 33 CNVs harboring 50 or more SNP eQTLs that predict the expression of a transcript (Table S1 lists these CNVs based on the number of SNP eQTLs within); these CNVs show an average SNP eQTL density of 6 per 10 kb.
