Genomic controls (Devlin et al., 2001) for the case-control phenotype were calculated with R-2.5.0 (http://cran.r-project.org) on a genome-wide level in the MARS GWAS sample. In addition, population stratification was tested with EIGENSTRAT implemented in EIGENSOFT (Price et al., 2006) (http://genepath.med.harvard.edu/~reich/EIGENSTRAT.htm). Neither the genomic control method (λ =1.023, see fig. S1) nor EIGENSTRAT analysis gave any indication for population stratification.
