The methylation correlation between human-specific TE insertions and their flanking regions. (A) Schematic representation of average methylation calculation of all insertions and associated 300 bp flanking regions. (B) Methylation correlation between insertions and 300 bp flanking regions. The average methylation of insertions is represented on the y-axis; the methylation of flanking regions, on the x-axis. Alu, LTR, L1, SVA, and non-TE insertions are represented by red, green, blue, purple, and gray dots, respectively, whereas non-TE insertions are labeled gray, serving as a background. Linear regression lines with standard errors are also plotted and labeled with the same color scheme. (C) Methylation correlation between insertions within CpG islands and 300 bp flanking regions. The average methylation of insertions are represented on the y-axis; the methylation of flanking regions, on the x-axis. Alu and non-TE insertions are represented in the same way as they are in B. (D) The WashU Epigenome browser views of an Alu insertion between hypomethylated and hypermethylated regions. The insertion was absent from HG03516 paternal haplotype but present in all the other nine haplotypes. A genome-align track is used to illustrate the insertion site. The Alu insertion methylation is boxed, showing a gradual change of methylation from left to right. Both HiFi and ONT methylC tracks display a methylation percentage from 0% to 100%. (E) Schematic representation of insertion-flanking methylation regression as a function of insertion-flanking distance. For each distance from 100 bp to 10 kb, we performed linear regression between insertion and flanking average methylation and estimated the linear regression slope and standard errors. (F) Linear regression slope between insertion and flanking methylation as a function of the insertion-flanking distance from 10 kb upstream to 10 kb downstream. Standard errors were represented by error bars. Alu, LTR, L1, SVA, and non-TE insertions are plotted in separated plots with different colors.