Fig. 4: Illustration of fine-mapping results in the region of MYH9-CSF2RB.

a Manhattan plot of the single-trait GWAS of milk yield (left) and protein percentage (middle), and multi-trait meta-analysis GWAS of 34 traits (right). Dot colour indicates variant membership to different clusters (putatively representing independent QTLs) defined by Eq. (1). b Posterior probability (PP) of individual variants from BayesRC runs of milk yield (left) and protein percentage (middle) and the sum of PP across BayesRC runs of 34 traits (right). c Summed PP of variants within each chromosome segment (grey line) and the variance of local gEBV for each segment (red line) for milk yield (left), protein percentage (middle) and for 34 traits combined (right). d \({\mathrm{Var}}_{g_{{\mathrm{local}}}}\left( {{\mathrm{variant}}} \right)\) for milk yield (left), protein percentage (middle) and for 34 traits combined (right). Black bars on the x-axis are genes labelled in (e). e FAETH⁷ annotated data of the right panel of (d). Large orange points are variants prioritized in the 80k selection and large red diamonds are variants prioritized in the 80k as well as having p < 0.05 in the US GWAS. Three variants that are prioritized by the Australian 80k selection and have p < 0.05 in the US GWAS are also splicing sQTLs in an Australian RNA sequencing dataset²⁸; the target genes (shown in red colour parenthesis) of these sQTLs have altered intron excision ratio (FDR < 0.05). Variants in the region that are conserved across 100 vertebrate species (conserved100w) and are historically young⁷ are also labelled.