We identified 12 traits with CNS enrichment at FDR<5% in our gene expression and/or chromatin analyses (Online Methods). We first investigated whether some brain regions are enriched over other brain regions for these traits using gene expression data from GTEx (Figure S7, Online Methods). The results are displayed in Figure 4a and Table S8a. We identified significant enrichments in the cortex relative to other brain regions at FDR<5% for bipolar disorder, schizophrenia, depressive symptoms, and BMI, and in the striatum for migraine. These enrichments are consistent with our understanding of the biology of these traits46–49, but to our knowledge have not previously been reported in any integrative analysis using genetic data. We also identified enrichments in cerebellum for bipolar disorder, years of education, and BMI. However, we caution that differential gene expression in samples from different brain regions can reflect the cell type composition of these brain regions as well as their function. In particular, the cerebellum is known to have a very high concentration of neurons50, and thus cerebellar enrichments could indicate either that the cerebellum is a region
