We used Decon-QTL19 to identify ieQTLs for the 25,497 independent Cortex-EUR cis-eQTLs: 3,549 cis-eQTLs (13.9%) showed at least one significant ieQTL (4,095 ieQTLs; Benjamini–Hochberg false discovery rate (BH-FDR) < 0.05; Supplementary Table 8). The largest group of interactions were with excitatory, inhibitory and other neurons (1,627; 39.7%), probably because neurons are the most prevalent cell type. The majority of the ieQTLs (3,090; 75.5%) were uniquely mapped to one cell type (Fig. 4c), although we cannot exclude the possibility that these ieQTLs are also present in other cell types.
