The results of our eQTL studies, previously on single base polymorphisms [10], [17], [18], in HapMap LCLs have been made publicly available in an online database SCAN [12]. To evaluate the influence of CNVs on the transcriptome, we performed linear regression on over 13,000 transcript clusters with reliable expression – namely, the log2 transformed normalized expression intensity is greater than 6 for at least 80% of the samples – and the CNVs assayed in HapMap LCLs. We downloaded genotype information for these CNVs from the recently released reference catalog of HapMap CNVs [7]. All eQTL analyses were done in both CEU and YRI samples. We extended the SCAN database to include a catalog of expression-associated CNVs in the HapMap populations.
