The exploration of quantitative variation in human populations has become one of the major priorities for medical genetics. The successful identification of variants that contribute to complex traits is highly dependent on reliable assays and genetic maps. After introducing Illumina's bead array technology for measuring expression levels, I will describe a genome-wide quantitative trait analysis of 630 genes in cell lines from 60 unrelated CEU individuals using the publicly available phase I data of the International HapMap project. The genes are located in regions of the human genome with elevated functional annotation and disease interest including the ENCODE regions spanning 1% of the genome, chromosome 21 and chromosome 20. Our results suggest that regulatory polymorphism is wide-spread in the human genome and show that the 5 kb (phase I) HapMap hassufficient density to allow linkage disequilibrium mapping in humans. Such studies will significantly enhance our ability to annotate the non-coding part of the genome and interpret functional variation.
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