Genetic interaction analysis of NKCC1 and DISC1 included three independent sample cohorts of cases with schizophrenia and healthy controls collected from Scotland, Germany and the United States (Table S2). The Scottish and German samples were genotyped using the Illumina 330K platforms. All SNPs in these two genes contained on this SNP platform were used in our genetic analyses. Pair-wise interaction analyses were carried out between SNPs in NKCC1 (rs10067555 and rs10089) and the SNPs in DISC1 (Table S2B) first in the Scottish sample, and the other two sample cohorts were used as replication samples to control for false positive findings. Logistic regression based on an additive model was used to assess the two-SNP interactions in each sample separately (Table S2C). The combined sample of all three cohorts together was also analyzed while controlling for sex and sample cohorts (Table S2A). To gain maximal power for interaction analysis, we combined genotypes at both SNPs into binary variables. Odds ratios (OR) were calculated for interaction at minor allele carriers of the two SNPs verse all other genotypes, and a likelihood ratio test
