We found male and female recombination rate to be strongly associated with density of H3K4me3 marks (Fig. 6a, Supplementary Fig. 17), and that H3K4me3 marks containing at least one degenerate PRDM9 motif are more recombinogenic in both sexes than those lacking a motif (Fig. 6b). H3K4me3 marks in testis are not all interchangeable to the marks associated with transcription in other tissue. The H3K4me3 marks specific to testis show increased rate in both sexes compared to marks seen in other ENCODE tissues alone (Fig. 6c), while H3K4me3 marks found in other ENCODE cell lines but not in testis show no effect on the recombination rate at all. As such, we predict at least some overlap in H3K4me3 marks between spermatocytes and oocytes during the initialization of recombination, likely due to PRDM9 action.