leading to marked differences in observed expression. The gene deletion is rare among European and African populations but common in those of East Asian ancestry (Fig. 11.6) (Xue et al. 2008).

These data raise the question of the extent to which fine scale nucleotide diversity and copy number variation underlie the observed eQTLs. Stranger and colleagues analysed copy number variation for association with gene expression in the same HapMap populations as they analysed SNP markers and found significant but distinct associations, which were fewer in number but comparably reproducible across populations (Section 4.3) (Stranger et al. 2007a). Many more associations are likely to be found as our ability to resolve and quantify smaller scale copy number variation improves. The study reinforced the need to consider both fine scale nucleotide level diversity and structural genomic variation when analysing genetic determinants of gene expression, and in particular that analysis of either SNPs or copy number variants alone would capture a small minority of the associations due to the untyped class of genetic variation (Stranger et al. 2007a).

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