Complex networks of molecular phenotypes—gene expression (mRNA, ncRNA, miRNA, and so on), protein expression, protein state, and metabolite levels—respond more proximally to DNA variations that lead to variations in disease-associated traits. These intermediate phenotypes respond to variations in DNA that in turn can induce changes in disease associated traits. Because a majority of single nucleotide polymorphisms (SNPs) detected as associated with disease traits from the recent wave of genome-wide association studies (GWASs) do not appear to affect protein sequence, it is likely that these SNPs either regulate gene activity at the transcript level directly or link to other DNA variations involved in this type of regulatory role. Therefore, to uncover the genetic determinants affecting expression in a metabolically active tissue that is relevant to the study of obesity, diabetes, atherosclerosis, and other common human diseases, we profiled 427 human liver samples on a comprehensive gene expression microarray targeting more than 39,000 transcripts, and we genotyped DNA from each of these samples at 782,476 unique SNPs. The relatively large sample size of this study and the large number of SNPs genotyped
