Fig. 3: Summary of the identification of causal gene-tissue pairs and direct causal variants.

A, B The number and proportion of causal and likely novel causal gene-tissue pairs identified by TGVIS and TGFM, respectively. Likely novel gene-tissue pairs are defined as those do not present in the list of significant gene-tissue pairs identified by univariable S-PrediXcan (P < 0.05/20000). The proportion refers to the average number of causal and likely novel causal gene-tissue pairs per locus. C The number and proportion of direct causal variants identified by TGVIS and TGFM. D The distribution of the number of traits affected by causal gene-tissue pairs. E, F The distributions of scores for FathmmXF and Encode H3K9me3Sum annotations. Raincloud plots illustrate four classes: direct causal variants and xQTLs of causal gene-tissue pairs identified by TGVIS and TGFM. Pairwise Wilcoxon signed-rank test P values (two-side) are displayed at the top, while medians of annotation scores are shown at the bottom. The median was shown as a black bar. The lower and upper hinges corresponded to the 25th and 75th percentiles. The “sample sizes” in the test are the numbers of variants, which are 1256, 4787, 9552, 19057 for TGVIS (direct causal variant), TGVIS (xQTL of gene-tissue pairs), TGFM (direct causal variant), TGFM (xQTL of gene-tissue pairs), respectively. Source data are provided as a Source Data file. The figure was created in BioRender. Yang, Y. (2025) https://BioRender.com/b65f9a0.