After integrating GWAS findings with the 10x Genomics dataset, we leveraged cell type enrichment analyses by using the KI dataset, which is distinct from the 10x Genomics dataset because of its better coverage, higher resolution, and higher specificity to identify cell type-specific gene expression markers. Therefore, considerably more cell types were identified on a deeper cellular level with the KI dataset. The largest degree of consistency across methods in brain-related traits was found for SCZ and cognitive performance (Figs. 2 and 3, Figs. S18, S19, Table S12). Genetic loci that are associated with SCZ consistently mapped to excitatory pyramidal cells (CA1 and SS), while those associated with cognitive performance only mapped to pyramidal cells (SS). For SCZ, we found evidence by two methods that MSNs were the main implicated inhibitory neurons. MSNs and both types of pyramidal cells were found to be associated with cross-disorders by two methods, while only pyramidal cells were associated with educational attainment, and MSNs and pyramidal cells (CA1) were implicated in bipolar disorder. Suggestive findings are reported in the Supplementary Results.
