Fig. 5

Spatial locations of significant lipid trait signal variants in CD36 and PGM1, and tree diagrams for the defined windows and associated p-values. a Two variants in CD36 (Y325*, Y348F; PDB: 5LGD) significantly associated with HDL are in a signal region that is involved in oxidized low-density lipoproteins binding. These variants are nearby in protein space, but they are 825 bp apart on the chromosome (hg19.chr7:80300449 and hg19.chr7:80301274) with two variants between them. b Three variants in PGM1 (Y420H, V525F, M535V; PDB: 6BJ0) significantly associated with TRIG are on the periphery of the C-terminal “domain 4” involved binding the substrate phosphate, suggesting that they may modulate activity, but not entirely disrupt binding. These variants are close in protein space, but they are more than 10 kb apart along the chromosome (hg19.1:64114301, hg19.1:64120111, hg19.1:64125260), with three other variants between them in this interval. In protein structures (left panel), the purple spheres represent signal variants and cyan spheres represent non-signal variants. The right panel shows tree diagrams representing the defined windows. The windows with gray nodes are omitted because their cumulative minor allele counts are less than 10. The other windows are colored red that reflect the magnitudes of the p-values from testing the mean effects. The nodes corresponding to signal regions detected by PSCAN-M are marked by purple stars