Fig 8. Replication of exome variant.

rs28929474 is a missense variant on chromosome 14 in gene SERPINA1, low-frequency (MAF = 2.3%), imputed summary statistics (P_SSimp = 1.06×⁻¹³), replication in the UK Biobank (P_UKBB = 6.49×⁻⁷⁸). rs112635299 has the strongest signal in this region (P = 4.21 × 10⁻¹⁴), but is highly correlated to rs28929474 (LD = 0.95). This figure shows three datasets: Results from the HapMap and the exome chip study, and imputed summary statistics. The top window shows HapMap P-values as orange circles and the imputed P-values (using summary statistics imputation) as solid circles, with the colour representing the imputation quality (only ${\widehat{r}}_{\text{pred,adj}}^2\ge 0.3$ shown). The bottom window shows exome chip study results as solid, grey dots. Each dot represents the summary statistics of one variant. The x-axis shows the position (in Mb) on a ≥ 2 Mb range and the y-axis the −log10(P)-value. The horizontal line shows the P-value threshold of 10⁻⁶ (dotted) and 10⁻⁸ (dashed). Top and bottom window have annotated summary statistics: In the bottom window we mark dots as black if it is are part of the 122 reported hits of [13]. In the top window we mark the rs-id of variants that are part of the 122 reported variants of [13] in bold black, and if they are part of the 697 variants of [12] in bold orange font. Variants that are black (plain) are imputed variants (that had the lowest conditional P-value). Variants in orange (plain) are HapMap variants, but were not among the 697 reported hits. Each of the annotated variants is marked for clarity with a bold circle in the respective colour. The genes annotated in the middle window are printed in grey if the gene has a length < 5′000 bp or is an unrecognised gene (RP-).