As noted above, the pattern of associations of psychiatric and cognitive traits were highly correlated across the 39 different cell types tested (Figure S6). For example, the Spearman rank correlation of cell type associations (−log10P) between schizophrenia and intelligence was 0.96 (0.94 for educational attainment) as both traits had the strongest signal in telencephalon projecting excitatory neurons and little signal in immune or vascular cells. In addition, we observed that genes driving the association signal in the top cell types of the two traits were enriched in relatively similar GO terms involving neurogenesis and synaptic processes. We evaluated two possible explanations for these findings: (a) schizophrenia and intelligence are both associated with the same genes that are specifically expressed in the same cell types or (b) schizophrenia and intelligence are associated with different sets of genes that are both highly specific to the same cell types. Given that these two traits have a significant negative genetic correlation (rg=−0.22, from GWAS results alone) (Figure S2 and Table S1), we hypothesized that the strong overlap in cell type associations for schizophrenia and intelligence was due to the second explanation.
