Fig. 3

Examples of cancer and non-cancer cell lines from SNP and ChIP-seq ENCODE data. a B allele frequencies (BAFs) for chromosome 1 for three cancer cell lines (MCF-7, K562, and SK-N-SH) and one non-cancer cell line (GM12878). Individual SNPs are colored according to genotype values: homozygous AA or BB (blue) and heterozygous AB (orange). b Correlations between the BAF values and the ChIP-seq AR of heterozygous SNPs. RAF corresponds to the BAF value with respect to the reference allele (RAF is equal to BAF if the reference allele corresponds to the B allele; RAF is equal to 1 − BAF if the reference allele corresponds to the A allele). The fitted linear model (blue line) and the Spearman correlation coefficient (cor) show the relationship between BAF and ChIP-seq ARs at heterozygous sites. AR allelic ratio, BAF B allele frequency, chr1 chromosome 1, cor correlation, RAF reference-allele frequency, SNP single-nucleotide polymorphism