Fig. 2
Summary of the results of EWAS in the discovery phase. a Quantile-quantile (QQ) plot. Observed (y-axis) versus expected (x-axis) p-values using a linear regression model. The λ value (inflation factor) was estimated from the median of the observed versus expected p-values. b Manhattan plot. Negative logarithm of the p-values (-log10(p-value)) versus chromosomal positions. Genome-wide significance threshold (red line): Bonferroni corrected p < 1.59 × 10−8. Suggestive threshold (blue line): p < 1.00 × 10−6. c Locus zoom plot of the DNAm levels and genetic regulatory elements in PCBD2/MTND4P12 gene. The region of Chr5:134923256-134928594 around the six ccRCC-associated DNAm markers (the region squared by the magenta line) was populated with DNase I hypersensitive sites (DHS), transcription factor binding sites, CCCTC binding factors binding sites. CTCF, CCCTC-binding factor; DHS, DNase I high sensitivity site; TF, transcription factor binding site; EWAS, epigenome-wide association study; DNAm, DNA methylation