To characterize the genetic architecture of gene expression in human liver, we compiled a tissue-specific human liver cohort (HLC), which comprised 427 Caucasian subjects (Table S1). DNA and RNA were isolated from all liver tissue samples. Each RNA sample was profiled on a custom Agilent 44,000 feature microarray composed of 39,280 oligonucleotide probes targeting transcripts representing 34,266 known and predicted genes, including high-confidence, noncoding RNA sequences. Each DNA sample was genotyped on the Affymetrix 500K SNP and Illumina 650Y SNP genotyping arrays. Analysis was restricted to those SNPs that had a genotyping call rate greater than 75%, a minor allele frequency greater than 4%, and that did not deviate significantly from Hardy-Weinberg equilibrium in the HLC. A total of 310,744 and 557,240 SNPs met these criteria from the Affymetrix and Illumina sets, respectively, resulting in a set of 782,476 unique SNPs (85,508 SNPs were in the intersection), referred to here as the analysis SNP set.
