For brain-related traits (Figure 1C, S4 and Table S2), 13 of 18 traits were significantly associated with one or more GTEx brain regions. For example, schizophrenia, intelligence, educational attainment, neuroticism, BMI and MDD were most significantly associated with brain cortex, frontal cortex or anterior cingulate cortex, while Parkinson’s disease was most significantly associated with the substantia nigra (as expected) and spinal cord (Figure 1C). Alzheimer’s disease was associated with tissues with prominent roles in immunity (blood and spleen) consistent with other studies 25–27, but also with the substantia nigra and spinal cord. Stroke was associated with blood vessel (consistent with a role of arterial pathology in stroke) 28. Traits with no or unexpected associations could occur because the primary GWAS had insufficient sample size for its genetic architecture 29 or because the tissue RNA-seq data omitted the correct tissue or cell type.
