Fig. 1

Recombination valleys within genetic, physical, and activity links. Example genomic regions to show the enrichment of a meQTL pairs (red), b eQTL pairs (orange), c top 10% Hi-C pairs (observed/expected (O/E), no CTCF motif, blue), d DNase–TSS pairs (no CTCF motif, purple) in low recombination rate regions. Each pixel represents a 10-kb segment (for Hi-C, a 1-kb segment) and darker color indicates higher recombination rate between two segments. Colored dots at each pixel indicate the genetic or physical links that exist between two genomic segments. The average recombination rate within e meQTL pairs (red), f eQTL pairs (orange), g top 10% of Hi-C pairs (O/E, no CTCF motif, blue), h DNase–TSS pairs (no CTCF motif, purple) are significantly lower than the matched random intervals. Colored lines represent the mean recombination rate at each interval distance between genomic features, while black links represent the mean value in matched random intervals. Shaded regions represent the 95% confidence interval (mean ± standard deviation × 1.96/10). Recombination rate in three different genomic scales in i meQTL pairs, j eQTL pairs, k top 10% of Hi-C pairs (O/E, no CTCF motif), l DNase–TSS pairs (no CTCF motif). Comparisons with p < 1e⁻⁴ (two-way paired Mann–Whitney U test) are marked with an asterisk