Extended Data Fig. 8: Causal variant enrichment for GWAS and comparison with published bulk methods and single-cell methods.
From: Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles
a. Comparison of the mean causal variant enrichment for FinnGen GWAS (y-axis) among SCENT (teal), EpiMap (red), and ABC model (blue) as a function of the number of significant peak-gene pairs (x-axis) at each threshold of significance. The bars indicate 95% confidence intervals by bootstrapping traits (nbootstrap=1000). b. We calculated the causal variant enrichment for FinnGen GWAS among SCENT (teal), EpiMap (reds), and ABC model (blues) by changing the PIP thresholds in defining putative causal variants from fine-mapping. The bars indicate 95% confidence intervals by bootstrapping traits (nbootstrap=1000). c and d. The mean causal variant enrichment for GWAS within SCENT enhancers (teal), ArchR (pink) and Signac enhancers (purple). GWAS results were based on FinnGen (c) and UK Biobank (d) using the FDR < 10% threshold in each software and eight benchmarking datasets (see Methods). The bars indicate 95% confidence intervals by bootstrapping traits (nbootstrap=1000).
