The analysis conditional upon SNPs was carried out using all of the centrally analyzed cohorts (Bipolar, Unipolar, COPD, KORA, POPGEN, Lausanne, LOLIPOP, GEMS, MEDSTAR, SHIP, WTCCC-CAD and WTCCC-HT). At the SNP being conditioned upon we used expected genotype counts as this allowed us to combine data from cohorts which had imputed the SNP and cohorts which had genotyed the SNP. These expected counts where included into the baseline null model as an additional covariate along with the other covariates such as Age, Sex and covariates coding for population structure. The same method was used when conditioning upon two SNPs. The model selection analysis of the two pairs of SNPs in the 15q25 region was carried out using the expected genotype counts. Analysis was carried out using the R statistical package.
