Fig. 1
Examples of previously unreported target gene predictions at known breast cancer risk loci. Variants are represented by points colored according to the LD with the sentinel risk variant (red: ≥0.8, orange: 0.6–0.8, green: 0.4–0.6, light blue: 0.2–0.4, and dark blue: <0.2). Sentinel risk variants (triangles) were identified based on joint association analysis9. Figure shows on the y-axis the evidence for breast cancer association (−log10 of the P-value in the original published GWAS results2, obtained in that study using an inverse-variance meta-analysis), and on the x-axis chromosomal position. Gene structures from GENCODE v19 gene annotations are shown and the predicted target genes shown in red. a The sentinel risk variant at this locus (rs875311) was in LD with sentinel eQTL for CFL1 (in whole blood) and for EFEMP2 (in CD8+ T cells only). b The sentinel risk variant (rs11049425, target gene: CCDC91) represents a secondary association signal in this region. c The sentinel risk variant at this locus (rs8105994) is in LD with sentinel eQTL for two previously unreported target gene predictions (AC010335.1 and LRRC25) and four previously predicted targets (CTD-3137H5.1, ELL, PGPEP1 and SSBP4; (Supplementary Data 5). Regional association plots for the remaining target gene predictions for overall breast cancer (Supplementary Data 3) are provided in Supplementary Figure 1
