Systematic Regulatory and Phenotypic Annotation of Candidate Chronic Post-Surgical Pain GWAS Loci

Background: Chronic post-surgical pain (CPSP) is a debilitating condition with evidence of genetic susceptibility. Most trait-associated variants identified by genome-wide association studies (GWASs) lie in non-coding regions, making functional interpretation challenging. Methods: This study systematically evaluated loci reported across five CPSP GWASs using linkage disequilibrium (LD) resolution, ENCODE4 candidate cis-regulatory element (cCRE) annotation, LD-proxy regulatory overlap analysis, CTCF motif scanning, and gene-level phenotypic association analysis. Results: Of 50 candidate lead genome-wide suggestive variants with a p-value < 10−6, four non-independent clusters were identified, yielding 45 independent loci for downstream analysis. Distal enhancer-like signatures were the most frequent nearest cCRE annotation, occurring at 29/45 loci (64.4%), but no cCRE class was significantly enriched relative to that at 500 random autosomal background positions. Lead SNPs directly overlapped a cCRE at 12/45 loci (26.7%); inclusion of high-LD proxies increased this to 19/45 loci (42.2%), identifying regulatory overlap at seven additional loci not captured by lead-SNP annotation alone. Fifteen loci had a CTCF-bound nearest cCRE, but only one contained a high-confidence canonical CTCF motif. Gene-level PheWAS classification yielded two Strong, 12 Moderate, four Indirect, and 27 None assignments; however, the Moderate-or-above rate was nearly identical to that of 500 random protein-coding genes (31.1% vs. 32.4%; Fisher’s exact p = 1.00). Conclusions: These findings indicate that currently reported CPSP loci do not show large-effect enrichment for a specific regulatory-element class or for genes previously associated with other pain phenotypes. The resulting catalog supports prioritizing individual loci for replication and functional validation, a prerequisite for any future use in preoperative risk stratification.