Table 1.

Filtering thresholds considered

Filter type	Thresholds considered
Distance to nearest mouse KnownGene TSS	⩽ {10000, 5000, 2000, 1000, 500, 200} base pairs
Distance to nearest mouse CAGE TU	⩽ {10000, 5000, 2000, 1000, 500, 200} base pairs
Mouse ES cell H3K4me3 density	⩾ {1, 2, 4, 8, 16, 32} arbitrary units
Mouse MEF cell H3K4me3 density	⩾ {1, 2, 4, 8, 16, 32} arbitrary units
Mouse NP cell H3K4me3 density	⩾ {1, 2, 4, 8, 16, 32} arbitrary units
Mouse masked phastCons score	⩾ {0.1, 0.2, 0.3, 0.5, 0.7, 1} arbitrary units
Distance to nearest human KnownGene TSS	⩽ {10000, 5000, 2000, 1000, 500, 200} base pairs
Human ES cell H3K4me3 density	⩾ {0, 0.1, 0.2, 0.5, 0.7, 1} arbitrary units
Human liver H3K4me3 density	⩾ {0, 0.1, 0.2, 0.5, 0.7, 1} arbitrary units
Human REH cell H3K4me3 density	⩾ {0, 0.1, 0.2, 0.5, 0.7, 1} arbitrary units
Human T-cell H3K4me3 density	⩾ {1, 2, 4, 8, 16, 32} arbitrary units

Units for each H3K4me3 density threshold are defined in section ‘Histone modification data’. Units for the masked phastCons score are defined in the ‘Phylogenetic conservation data’ section.