Genome-wide association studies have discovered hundreds of loci
associated with complex brain disorders, but it remains unclear in which
cell types these loci are active. Here we integrate genome-wide
association study results with single-cell transcriptomic data from the
entire mouse nervous system to systematically identify cell types
underlying brain complex traits. We show that psychiatric disorders are
predominantly associated with projecting excitatory and inhibitory
neurons. Neurological diseases were associated with different cell
types, which is consistent with other lines of evidence. Notably,
Parkinson's disease was genetically associated not only with cholinergic
and monoaminergic neurons (which include dopaminergic neurons) but also
with enteric neurons and oligodendrocytes. Using post-mortem brain
transcriptomic data, we confirmed alterations in these cells, even at
the earliest stages of disease progression. Our study provides an
important framework for understanding the cellular basis of complex
brain maladies, and reveals an unexpected role of oligodendrocytes in
Parkinson's disease.