Fig. 1: Significant cis-eQTLs, cis-pQTLs and their overlap.

a Circular plot of the significant cis-eQTLs (blue) and pQTLs (purple) at a FDR cutoff of 0.05 (dotted line, plot created using the R package circlize⁸⁵). Considering only genes with both transcriptomics and proteomics measurements, we visualized the overlap of significant eQTLs and pQTLs in the circle center. In total, the lead SNP-gene pair of 200 QTL clumps in 124 genes had a significant eQTL and 133 loci in 87 genes a significant pQTL. Only 19 lead variants (13 genes) had an eQTL and pQTL for the same gene. The numbers in brackets represent the number of significant SNP-gene pairs. b Characterization of overlapping eQTL and pQTL loci. All 19 LD clumps (based on eQTL and pQTL summary statistics) where the lead SNP-gene-pair was a significant eQTL and pQTL were classified as a shared QTL by either our residual regression approach or colocalization analysis. c Characterization of eQTL loci without a corresponding pQTL. Only 83 out of 181 LD clumps (based on eQTL and pQTL summary statistics) that had a lead SNP-gene-pair with a significant eQTL but no pQTL were classified as an independent eQTL by either our residual regression approach or colocalization analysis. d Characterization of pQTL loci without a corresponding eQTL. Only 42 out of 114 LD clumps (based on eQTL and pQTL summary statistics) that had a lead SNP-gene-pair with a significant pQTL but no eQTL were classified as an independent pQTL by either our residual regression approach or colocalization analysis. eQTL expression quantitative trait loci, pQTL protein quantitative trait loci, QTL quantitative trait loci, FDR false discovery rate, LD linkage disequilibrium, SNP single-nucleotide polymorphism. Source data are provided as a Source Data file.