Chunk #34 — Materials — Anticipated results — Visualising the tagSNPs in the context of PPARG and regional LD structure

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Marker selection for genetic case-control association studies.

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yes

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Figure 3 shows the tagSNP visualisation using GoldSurfer2 (step 12). The upper track with SNP marks shows all common (maf > 5%) HapMap SNPs in the region with rs1801282 highlighted in red. The second SNP track shows the coverage of the selected tagSNPs. The knownCanonical gene table from UCSC is cleaned for false hits and redundancies with the effect that only the suggested functional version of PPARG is visible in the plot. LD is measured in r2.