Figure 3 shows the results for LDLc levels. The pattern of results appeared similar to that for CRP in that the proportion of variance explained was greatest when the SNP inclusion threshold was conservative. In the case of the genome-wide scores including the known variants, the weighted score explained from 3.2% to 5.5% of the phenotypic variance in LDLc depending on the SNP inclusion threshold, whereas the unweighted score explained from 1.1% to 4.2% of the variance. The weighted score explained more of the phenotypic variance in LDLc than the unweighted score across all SNP inclusion thresholds tested. Similarly, the most variance in LDLc levels was explained using an allelic score derived from known variants only. When the known regions were removed from the construction of the scores, the most variance explained was obtained using cut-offs in the range 0.4<p<0.6, although the inclusion of extra genotype information decreased the scores' explanatory ability slightly.
