Figure 1
RCC-associated polymorphic loci overlap HIF-binding sites in RCC cells. (A) RCC-associated polymorphisms overlap HIF-binding sites in RCC cell lines. 4 out of 13 GWAS loci directly overlapped HIF-binding sites in RCC cells (red arrow). The blue bars denote the frequency distribution of the expected overlap in the bootstrapping approach when the GWAS loci were randomly shuffled around the genome 100,000 times. Significant enrichment (p = 7 × 10−5) of active enhancers at RCC-associated GWAS loci was observed. (B) HIF-binding enhancers were targeted in preference to those that do not bind HIF. The converse bootstrapping approach in which the HIF-binding sites were randomly shuffled, but constrained to regions defined as active enhancers, again showed that this overlap was significantly greater than expected (p = 6 × 10−5). Note that one of the RCC-susceptibility loci directly overlapped two HIF-binding sites. (C) RCC-associated polymorphisms are enriched in proximity to HIF-binding sites. 7 GWAS loci either overlapped or lay within 25 kb of a HIF-binding site. A similar bootstrapping approach, in which the number of shuffled loci lying within 25 kb of a HIF-binding site was used to determine the significance of the observed result (p = 1 ×10−5). (D–F) For comparison, the same analyses were performed using GWAS loci associated with educational achievement, which showed no significant enhancement for overlap with HIF-binding sites.
