Extended Data Fig. 4: QTL mapping of the different molecular traits.

(A) Proportion and number of SNP-QTL at a significance threshold of FDR < .10 in each condition (B) Proportion and number of STR-QTL at a significance threshold of FDR < .10 in each condition. (C) Proportion and number of genes/features associated with at least one SNP or STR QTL in non-infected macrophages. Shared QTL were defined as those genes/features associated with a QTL at an FDR < .10 when performing the QTL mapping against SNPs and STRs separately. SNP- or STR-specific are those only identified as significant (FDR < 0.1) against either SNPs or STRs. (D) The mean percent variance explained by the top SNP and STR across all features in the non-infected condition. Both is the sum of the PVE of the top SNP and top STR (E) The enrichment of TF binding sites across non-infected specific SNP-QTL using a logistic regression. TF clusters are shown. (See Supplementary Table 4 for full results).