Fourth, we highlight the importance of examining conditional eQTL for co-localization with GWASs. In at least 6 out of 40 loci showing GWAS-eQTL co-localization, a conditional eQTL signal co-localizes with SCZ risk. This is likely to be a conservative estimate, as the smaller effect sizes of conditional eQTL results in bias against detection of conditional GWAS-eQTL co-localization. If we had considered only primary eQTL in the analyses, these instances of co-localization would not have been identified. Among our highlighted conditional eQTL-GWAS co-localized genes are IREB2, STAT6, and PROX1-AS1. IREB2 (iron regulatory element binding protein 2) is a key regulator of iron homeostasis68, 69 that has been previously implicated in neurodegenerative disorders.70, 71 Mouse IREB2 homolog Irp2 knockouts exhibit impairments in coordination and balance, exploration, and nociception.69 The immune-related transcription factor STAT6 induces interleukin 4 (IL-4)-mediated anti-apoptotic activity of T helper cells, and the locus is associated with migraine72, 73 and brain glioma74 as well as several immune/inflammatory diseases.75, 76, 77 STAT6 also activates neuronal progenitor/stem cells and neurogenesis,78 making it intriguing as an immune-related SCZ candidate given recent observations about the role of complement factor 4 (C4) gene as a SCZ risk gene79 and prior work potentially implicating microglia.80 Consistent with a role in immune-mediated synaptic pruning, STAT6 expression is broadly postnatal and shows specificity for microglia (Table S8). PROX1-AS1 encodes a lncRNA that has been implicated as aberrantly expressed in several cancers, is upregulated in the cell cycle S-phase, and promotes G1/S transition in cell culture.81 As a potential regulator of the Prospero Homeobox 1 (PROX1) transcription factor, it could be involved in development and cell differentiation in several tissues, including oligodendrocytes82 and GABAnergic interneurons83 in the brain. PROX1-AS1 expression is specific to neurons and mature oligodendrocytes and is expressed postnatally (Table S8).