We resequenced the promoter and 3′UTR regions within the 60 UW liver samples and 35 CEU HapMap samples for 18 genes that showed strong expression-SNP correlations within the UW data (selected before replication information was available). We used PCR amplification and Sanger-sequencing, identifying SNPs using both automated prediction and manual curation as previously described (http://pga.gs.washington.edu/). 3′UTRs were defined using the appropriate gene models, while promoters were defined as the 1 kb segment upstream of the annotated transcriptional start site. We subsequently defined haplotypes within each promoter and 3′UTR as previously described using Phase [58], and designated as common all haplotypes present in at least two samples.
