As expected when the EIGENSTRAT analysis was performed using the entire SNP set, this showed strong evidence for association of the PTPN22, TRAF1 and the MHC SNPs. Similarly, when the ESAIMs were applied either using EIGENSTRAT or a method for structured association (STRAT), evidence for the association of these SNPs remained after controlling for population substructure (Table 3). For the LCT SNP in strong linkage disequilibrium with lactose intolerance the evidence for association (p < 5E−5) was no longer present when the entire 500K SNPs or ESAIMs were utilized in EIGENSTRAT (p > 0.05) or the STRAT analysis (p > 0.05).
