Figure 1 shows the PPARG genomic information displayed using the UCSC database by focussing on the region 40kb up and downstream of the RefSeq track NM_138712 (step 5). The LD structure for the CEU shows that the PPARG gene includes two blocks of high LD that expands approximately to the boundaries of the largest variant of the gene. Given that LD does not extend outside of the gene means that there is no need to increase the main interval within which we select our markers. Furthermore substantial cost reductions can be achieved by selecting tagSNPs from within the two large LD blocks. The SNPs captured by different commercially available panels are highlighted and with some of these designed using a tagging approach, it gives an idea about the result obtained by this approach and shows the applicability to use the genotype data from a GWA panel.
