Quantitative differences in gene expression are thought to contribute to phenotypic differences between individuals. We generated genome-wide transcriptional profiles of lymphocyte samples from 1,240 participants in the San Antonio Family Heart Study. The expression levels of 85% of the 19,648 detected autosomal transcripts were significantly heritable. Linkage analysis uncovered 41,000 cis-regulated transcripts at a false discovery rate of 5% and showed that the expression quantitative trait loci with the most significant linkage evidence are often located at the structural locus of a given transcript. To highlight the usefulness of this much-enlarged map of cis-regulated transcripts for the discovery of genes that influence complex traits in humans, as an example we selected high-density lipoprotein cholesterol concentration as a phenotype of clinical importance, and identified the cis-regulated vanin 1 (VNN1) gene as harboring sequence variants that influence high-density lipoprotein cholesterol concentrations. Phenotypic differences among individuals are partly the result of quantitative differences in transcript abundance. Although environmental stimuli may influence the location, timing, and/or level of transcription of specific genes, genetic differences among individuals are also known to have a significant role. Transcript levels may be thought of as quantitative endophenotypes that can be subjected to statistical genetic analyses in an effort to localize and identify the underlying genetic factors, an approach that is sometimes referred to as genetical genomics 1 . Using microarray technology, it is now possible to assess the abundance of many transcripts-and, indeed, of the entire known transcriptome-simultaneously. Studies that attempt to localize the genetic regulators of gene expression have been carried out in several species, including yeast 2-5 , plants (maize and eucalyptus) 6,7 , fly 8 , mouse 6,9,10 and rat 11 . Several recent investigations have also focused on humans. In most of these studies, microarray-based gene expression profiles were generated for transformed cell lines derived from lymphocytes from members of the Centre d'Etude du Polymorphisme Humain (CEPH) families 12 , and linkage and/or linkage disequilibrium approaches were used to map the genetic determinants that regulate the expression of individual transcript
