While large-scale genome-wide association studies (GWAS) have identified hundreds of loci associated with neuropsychiatric and neurodegenerative traits, identifying the variants, genes and molecular mechanisms underlying these traits remains challenging. Integrating GWAS results with expression quantitative trait loci (eQTLs) and identifying shared genetic architecture has been widely adopted to nominate genes and candidate causal variants. However, this integrative approach is often limited by the sample size, the statistical power of the eQTL dataset, and the strong linkage disequilibrium between variants. Here we developed the multivariate multiple QTL (mmQTL) approach and applied it to perform a large-scale trans-ethnic eQTL meta-analysis to increase power and fine-mapping resolution. Importantly, this method also increases power to identify conditional eQTL’s that are enriched for cell type specific regulatory effects. Analysis of 3,188 RNA-seq samples from 2,029 donors, including 444 non-European individuals, yields an effective sample size of 2,974, which is substantially larger than previous brain eQTL efforts. Joint statistical fine-mapping of eQTL and GWAS identified 301 variant-trait pairs for 23 brain-related traits driven by 189 unique candidate causal variants for 179 unique genes. This integrative analysis identifies novel disease genes and elucidates potential regulatory mechanisms for genes underlying schizophrenia, bipolar disorder and Alzheimer’s disease.