major depression (Hennah and Porteous 2009). There was good agreement between the top SNP associations (i.e., those located in genes) and the gene-based tests. That FHIT and RAVER1 were not significant in the gene-based test indicates that the SNP associations within these genes are possibly type 1 error, are in LD with another important gene, or have very specific effects on gene functioning, for instance if they are exonic SNPs.
