Abstract
<jats:p>Genetic fine-mapping identifies causal variants within trait-associated loci, but linkage disequilibrium (LD), and wide datasets complicate this sparse variable-selection problem. SuSiE is popular for its fast variational inference, posterior inclusion probabilities (PIPs), and credible sets, yet a single fit can fail to resolve LD ambiguity, converge to a poor local optimum, or misrepresent uncertainty over competing configurations. We introduce SuSiNE (Sum of Single Non-central Effects), a SuSiE extension incorporating signed functional annotations through a prior-mean channel, μ₀ = ca, while preserving effect conjugacy, credible sets, and summary-statistic sufficiency. The resulting single-effect Bayes factor self-gates on agreement between annotation sign and association direction, limiting annotation-noise influence. We show that the common final step of purity filtering can discard informative signal, and tends to hurt performance. We also introduce new effect-level diagnostics for concentration, accuracy, and fitted-basis movement, to provide deeper insights into model behavior. To explore and summarize multiple variational basins, we pair the model with grid-based ensembling and cluster-weight aggregation. In oligogenic simulations with annotations calibrated to AlphaGenome eQTL benchmarks, the ensemble raised pooled AUPRC for recovery of the largest-effect causal variants from a SuSiE-equivalent 0.2474 to 0.3130 (0.0656 delta, 95% paired-bootstrap CI [0.0591, 0.0722]). At 75% precision, recall rose from 11.9% to 19.3% (61.7% relative gain). AUPRC gains were robust across varying annotation quality and alternative sparse and diffuse architectures, while sufficiently strong null annotation-association alignment reversed the gains. In a GTEx Lung summary-statistic case study, SuSiNE placed nontrivial weight on annotation-informed fits at 7 of 20 loci and changed which variants received high PIP. ARSA showed the cleanest durable shift, whereas the large YDJC shift coincided with reference-LD discrepancy. An internal diagnostic found little evidence of strong annotation confounding in this panel. These analyses use reference rather than in-cohort LD, demonstrating method behavior rather than definitive variant-level discoveries.</jats:p>