Fig. 4: Effect sizes and significance of cis-pQTL are influenced by allele frequency and genomic proximity to the transcription start site.
From: Efficient candidate drug target discovery through proteogenomics in a Scottish cohort
A SNPs with lower minor allele frequency tend to have larger absolute effect sizes. cis (in red) and trans (in blue) associations are coloured separately to show the same L-shaped distribution. cis-pQTL are both more detectable and have higher effect size at lower allele frequencies than trans-pQTL. Variants with minor allele frequency <0.05 were excluded from this analysis. Effect sizes (beta) were calculated on rank-based inverse normal transformed protein level data. B Distribution of cis-pQTL association p values by distance to the transcription start site of the gene encoding the protein. Closer to the TSS, pQTLs tend to be more significant, with a corresponding increase in effect size. TSS transcription start site, pQTL protein Quantitative Trait Locus.
