Fig. 10
From: “Gap hunting” to characterize clustered probe signals in Illumina methylation array data
Relationship between DNA methylation (DNAm) clusters, identified by gap hunting at cg12162195, and local haplotypes among the same individuals. a Percent methylation at cg12162195 versus gap hunting-defined DNAm group. b Individual haplotypes sorted by gap hunting-defined DNAm group. Each column represents a genotyped SNP at a specific locus across all individuals with corresponding DNAm data. Each row denotes an individual’s local haplotype for the region that contains cg12162195. There are two rows per individual, one per haplotype. The arrow at the top of the plot depicts the location of cg12162195 within the haplotype region. Gap hunting-identified groups correspond to different sets of haplotypes; these methylation groups can be used as surrogates of these haplotype groups. c Depiction of variant locations relative to probe orientation. Blue color indicates the single-base extension site; black color denotes 450k probe; pink denotes the interrogated CpG site. Y-axis lists variants present in the dbSNP138 database with a frequency greater than 0.5% and validated in more than 200 people