We identified genotypes of the 143 individuals using our snATAC-seq data. For all cell types with at least one DEG, we tested variants overlapping cell type-specific open chromatin regions for an association with expression of nearby differentially expressed genes (see Online Methods). In nine of the eleven cell types tested, we found at least one gene containing a variant in our snATAC-seq data overlapping an open chromatin region that was associated with a differentially expressed GWAS-associated gene. Six cell types contained over 10 genes with such an eQTL (Fig. 5B), and some genes contained eQTLs in multiple cell types. For example, PPP2R3C, within a locus associated with PAU, was associated with an eQTL with a negative effect size at variant rs1056879 in oligodendrocytes, D1/D2 MSNs, and fast-spiking interneurons (Extended Data Fig. 7). PPP2R3C was expressed at lower levels in both cell types from individuals with AUD. Combined, these findings suggest that AUD is associated with downregulation of this gene’s expression. ADAL, in a locus positively associated with alcohol drinks/week, was differentially expressed in D1, D2, D1/D2 and fast-spiking neurons, with a cis-eQTL at rs3742971 negatively associated with ADAL expression in all four of these cell types (Extended Data Fig. 7).
