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In a GWAS study of Europeans, this variant was associated with total cholesterol and low density lipids, with significances of 1.5E-11 and 2.6E-10 respectively. Because this is a genome-wide association, a p-value of 5 * 10^-8 was set as the cut-off, this exceeds that threshold 100- to 1000-fold.
Positive betas of 0.145 and 0.157 (effect of variant in standard deviations) are reported associating the reference allele at this position (G, with a “causal allele frequency” of 0.92, see Table 2) with higher cholesterol and LDL levels. This means that this variant (A, which we find has an allele frequency of ~0.07). The amount of total LDL variance explained by all genes in the study was 1-5%; we treat this variant, which was the strongest effect found, as having “penetrance” of 1-2%.