Extended Data Figure 8: Functional assessment of regulatory variants at 1p36, 11p15 and 1p34 risk loci.

a, b, The KLHDC7A (a) or PIDD1 (b) promoter regions, containing the reference (prom-Ref) or risk alleles (prom-Hap), were cloned upstream of the pGL3 luciferase reporter gene. MCF7 or Bre-80 cells were transfected with constructs and assayed for luciferase activity after 24 h. The means and 95% confidence intervals are shown. (n = 3). P values were determined by two-way ANOVA followed by Dunnett’s multiple comparisons test (*P < 0.05, **P < 0.01, ***P < 0.001). c, 3C assays. Top, a physical map of the region analysed by 3C. Grey boxes depict the PREs, blue vertical lines indicate the risk-associated SNPs and the black dotted line represents chromatin looping. Bottom, graphs representing three independent 3C interaction profiles. 3C libraries were generated with EcoRI, grey vertical boxes indicate the interacting restriction fragment (containing PRE1 and PRE2). Means and standard deviations are shown. d, PRE1 or PRE2 containing the reference (PRE-ref) or risk (PRE-Hap) haplotypes were cloned downstream of a CITED4 promoter-driven luciferase construct (CITED4 prom). MCF7 or Bre-80 cells were transfected with constructs and assayed for luciferase activity after 24 h. Error bars denote 95% CI (n = 3). P values were determined by two-way ANOVA followed by Dunnett’s multiple comparisons test (**P < 0.01, ***P < 0.001).