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Fig. 5 | Genome Biology

Fig. 5

From: NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

Fig. 5

Example of how to use the long-range allele-specific GCH methyltransferase footprint to annotate the allelic imbalance activities of GWAS variants. ChromHMM states in GM12878 are downloaded from the NIH Epigenome Roadmap. −log10 p value of IBD GWAS results are obtained from https://www.ibdgenetics.org/. Only high-quality long-range linked reads (>20kb distance) that overlapped with the chr5:13155245 locus are shown in the figure. The transparency of green color represents the methylation level of GCH in the reads: 100% opacity represents 100% GCH methylation in the reads. Fisher’s exact test is utilized to calculate the p value of GCH methylation differences between reference alleles and alternative alleles in SNP anchors and non-SNP anchors

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