Using eQTL results as an example (n=494, two-tailed), we examined the potential specificity of each lead eQTL SNP for five cell types that are abundant in the cortex: neurons, microglia cells, astrocytes, oligodendrocytes, and endothelial cells. We found that assignment to a single cell type is ambiguous for most eQTLs (p-values available at http://mostafavilab.stat.ubc.ca/xQTLServe). In a minority of cases, our analysis returned an unambiguous cell type for the lead eQTL. For example, at an FDR<0.05, we identified 6 significant cell-specific eQTLs (1 astrocytic, 3 microglia, and 1 neuronal). An example is presented in Figure 5C. The CPVL locus harbors an eQTL effect (rs11971828) that is stronger in microglial cells. With a more lenient discovery strategy where we thresholded the interaction term at an FDR<0.2, we found putative cell-type specific effects in neurons (n=13) and microglia (n=22) (Figure 5B). Even though only a small number of cell-specific eQTLs were identified with multiple testing correction, our results can still be useful in prioritizing cell types for follow-up experiments based on the observation that suggestive cell-type specific eQTL genes show clear cell type
