Fig. 5: Functionally informed fine-mapping across 49 tissues.
a The number of additional putative causal eQTLs (defined by PIPEMS > 0.9 and PIPunif < 0.9) for each tissue is shown in descending order. b–d Mean Basenji score in different classes of tissue-specific putative causal eQTLs for tissue-specific TF-related Basenji features for liver (b), whole blood (c), and LCLs (d). In 39 out of all 42 features across all three tissues, the mean Basenji score in tissue-specific putative causal eQTLs identified by PIPEMS is significantly higher in the corresponding tissue than in control tissues (t test p < 0.05/42). This changes to 36 in 42 when using PIPunif instead of PIPEMS. The enrichment of mean Basenji score in putative causal eQTLs in the corresponding tissue compared to control tissues is higher for PIPEMS than PIPunif for all 42 tissues (p < 10−100 in aggregate), consistent with our understanding that functionally informed fine-mapping using EMS utilizes cell-type-specific functional enrichments, identified from putative causal eQTLs identified with a uniform prior, to identify additional putative causal eQTLs. Duplicated names are distinct features corresponding to biological replicates in the TF activity measurements. Out of 17,960 tissue-specific putative causal eQTLs, n = 222 were for liver (b), n = 1758 were for whole blood (c), and n = 140 were for LCL (d).
