We then used gene set enrichment analysis (GSEA) and cross-tissue transcriptome-wide association study (TWAS) analyses with S-PrediXcan and Genotype-Tissue Expression (GTEx) version 8 prediction models.<h4>Results</h4>The synaptic pruning gene set reached Bonferroni-corrected significance in allergic diseases (p = 6.75 × 10−5), driven by major histocompatibility complex (MHC) class I genes (HLA-B, HLA-A, HLA-C, TAP2), complement genes (C4A, C4B), and inflammatory regulators (NFKB1, RELA). Here, HLA-C is linked to allergic disease.