Data analysis was conducted using the Ricopili pipeline19, including stringent quality control of genotyped variants and individuals (Methods). Information about non-genotyped markers was obtained by imputation using the 1000 genomes phase 3 as reference panel. GWAS was performed using imputed marker dosages and an additive logistic regression model using the following covariates: relevant principal components to correct for confounders such as population stratification, presence of the major psychiatric disorders studied in iPSYCH and genotyping wave. Only markers with an imputation INFO score >0.7, minor allele frequency (maf) >0.01 and bi-allelic variants were retained, in total 8,971,679 genetic variants were included. We identified 26 genome-wide significant variants (P<5x10−8), located in a single locus on chromosome 8 (Figure 1 and 2). The index variant, rs56372821, showed an odds ratio of 0.73 (P=9.31x10−12) with respect to the minor allele A (Table 1, Figure 1 and 2). We found no signs of contributions from confounding factors like population stratification and cryptic relatedness to the inflation in the distribution of the test statistics (lambda=1.033; see quantile-quantile plot, Figure 1.B.) using LD score regression, since the
