The anchor-matched ranking, run: the KMT2A exon-11 CTCF anchor is rank 58 of 1,625 anchors matched on baseline strength - the 3.6th percentile - and the matched MEDIAN anchor also falls to 0.63x, so 'CTCF falls only at the KMT2A anchor' is refuted while 'the KMT2A anchor loses more than most' survives weakly

[
  "GSM6431023",
  "GSM6431025",
  "GSM6431019",
  "GSM6431021"
]

{
  "summit_bin_start_hg19": 118359400,
  "summit_grch38": 118488685,
  "bp_from_the_independently_measured_summit_118488694": 9,
  "window_hg19": "chr11:118,359,000-118,360,000",
  "baseline_strength_S": 4.916,
  "S_percentile_among_all_anchors": 0.917,
  "ratio_R": 0.396,
  "per_track_window_means_normalised": {
    "GSM6431023_control": 6.507,
    "GSM6431025_control": 3.325,
    "GSM6431019_siKDM3B": 1.708,
    "GSM6431021_siKDM3B": 2.19
  },
  "both_kd_below_both_ctrl": true
}

{
  "M1_S_within_10pct": {
    "n": 1625,
    "rank": 58,
    "percentile": 0.0357,
    "median_R": 0.633,
    "iqr_R": [
      0.531,
      0.751
    ],
    "n_R_le_0.5": 308,
    "n_R_le_0.4": 64,
    "n_R_le_0.3": 5,
    "S_range": [
      4.425,
      5.407
    ]
  },
  "M2_nearest_500_in_S": {
    "n": 500,
    "rank": 22,
    "percentile": 0.044,
    "median_R": 0.622,
    "n_R_le_0.5": 100,
    "n_R_le_0.4": 24
  },
  "M3_strength_decile_10": {
    "n": 1245,
    "rank": 61,
    "percentile": 0.049,
    "median_R": 0.615,
    "n_R_le_0.5": 262,
    "n_R_le_0.4": 64,
    "S_range": [
      4.784,
      14.056
    ]
  },
  "ALL": {
    "n": 12443,
    "rank": 258,
    "percentile": 0.0207,
    "median_R": 0.696,
    "iqr_R": [
      0.58,
      0.827
    ]
  }
}

{
  "n_R_le_0.9": 10521,
  "n_R_le_0.7": 6325,
  "n_R_le_0.5": 1436,
  "n_R_le_0.5_and_both_reps_consistent": 1401,
  "n_R_le_0.4": 280,
  "n_R_le_0.3": 20,
  "paper_reports_for_comparison": "17,077 CTCF peaks losing intensity, of which 1,005 KDM3B co-occupied (PMID 37788669) - a different quantity computed a different way, same order of magnitude, same direction"
}

[
  0.779,
  0.751,
  0.731,
  0.731,
  0.714,
  0.694,
  0.672,
  0.653,
  0.64,
  0.615
]

{
  "calling_and_S_from": "GSM6431023",
  "ratio_denominator": "GSM6431025",
  "n_anchors": 9851,
  "kmt2a_R": 0.586,
  "M1": {
    "n": 185,
    "rank": 59,
    "percentile": 0.319,
    "median_R": 0.685
  },
  "ALL": {
    "n": 9851,
    "rank": 2925,
    "percentile": 0.297
  },
  "why_it_moves": "the two control replicates differ two-fold at this element, so the denominator choice changes the KMT2A ratio from 0.300 (rep1 alone) through 0.396 (mean) to 0.586 (rep2 alone); and a one-replicate denominator adds independent noise to every anchor's R, compressing the distribution and making everything look less extreme"
}

{
  "2.5": 0.0357,
  "3.0": 0.0357,
  "4.0": 0.0357,
  "5.0": 0.0358
}

{
  "exon11_canonical": {
    "measured": 0.301,
    "published": 0.3
  },
  "ctcf_summit_pm250": {
    "measured": 0.319,
    "published": 0.32
  },
  "element_ctcf_cluster": {
    "measured": 0.401,
    "published": 0.4
  },
  "cut_point_pm250": {
    "measured": 1.021,
    "published": 1.02
  },
  "kmt2a_gene_90kb": {
    "measured": 0.956,
    "published": "not reported"
  }
}

{
  "only_at_the_kmt2a_anchor": "REFUTED - 15-19% of strength-matched anchors fall to 0.5x or below, the matched median is 0.62-0.70 rather than 1.0, and 84.6% of all 12,443 anchors are at or below 0.9x",
  "exceptional_in_degree": "WEAKENED to a range - 3.6th percentile in the primary matched analysis, 31.9th under the pre-declared bias control, bracketed and not narrowable at n = 2 per arm",
  "the_locus_address_sits_on_the_ctcf_arrow": "DOES NOT SURVIVE - the CTCF arrow is genome-wide too, so neither the mark arrow nor the CTCF arrow carries a locus label in these data",
  "hyp_the_kmt2a_anchor_is_hypersensitive_not_uniquely_targeted": "CONFIRMED on its own stated prediction - a continuous distribution with 1,436 anchors below 0.5x and KMT2A at the 2.07th percentile, not an outlier separated from a bulk near 1.0x; its falsifier did not fire"
}

{
  "THE_STATED_GRCh38_COORDINATE_IS_WRONG": "This beat states 'hg19 chr11:8,241,000 = GRCh38 chr11:8,370,285'. That is wrong. 8,370,285 - 8,241,000 = 129,285, which is the GRCh37->GRCh38 offset at the KMT2A locus at 118.4 Mb; it was applied here as though the offset were constant along chromosome 11, and it is not.",
  "the_correct_lift_measured_by_the_king_2026_09_22": {
    "hg19 chr11:8,241,000": "GRCh38 chr11:8,219,453, offset -21,547",
    "controls proving the offset varies": {
      "hg19 chr11:8,000,000": "GRCh38 7,978,453, offset -21,547",
      "hg19 chr11:50,000,000": "GRCh38 49,978,464, offset -21,536",
      "hg19 chr11:118,358,874 (the KMT2A element)": "GRCh38 118,488,159, offset +129,285"
    },
    "so": "the offset is locally constant but varies by more than 150 kb along chromosome 11 and changes sign; a single locus's offset is never transferable to another locus",
    "source": "Ensembl REST map/human/GRCh37/11:start..end:1/GRCh38, filtered on seq_region_name == '11'"
  },
  "NOTHING_MEASURED_IS_AFFECTED": "The GSE210480 CTCF bigWigs declare exactly hg19 and the whole 12,443-anchor ranking was computed in hg19. Every strength, ratio, rank and percentile in this beat stands. The error is confined to a convenience coordinate quoted for the reader.",
  "AND_THE_COMPARATOR_IS_NOW_ANNOTATED_AT_THE_CORRECT_POSITION": {
    "why_this_is_here": "this beat's own caveat said 'the chr11:8,241,000 comparator has not been annotated: what gene or element it sits in was not looked up'. It has now been looked up - at the corrected position, because the first attempt used the wrong one.",
    "GRCh38 chr11:8,219,453 overlaps": "lncRNA ENSG00000307368, 8,202,758-8,224,376",
    "LMO1 (protein_coding, 8,224,309-8,268,807)": "4,856 bp away",
    "other features within 50 kb": "ENSG00000307401 lncRNA 9,812 bp; ENSG00000307386 lncRNA 12,986 bp; RIC3-DT lncRNA 39,206 bp",
    "THE_COMPARATOR_IS_NOT_INERT": "LMO1 is an established T-lineage oncogene and neuroblastoma susceptibility gene, and the anchor sits 4.9 kb from it inside a lncRNA. So this is NOT the featureless intergenic control the proposal implies. It remains a valid STRENGTH-matched comparator - that was the matching criterion and it holds - but 'a strong anchor that loses more CTCF than KMT2A and has no disease relevance' is not something this annotation supports.",
    "what_is_still_unchecked": "the beat's other caveat stands and is not addressed here: whether this anchor is in a blacklist region or a segmental duplication was not tested, and a strong anchor with a large apparent change is what a blacklist artefact looks like"
  },
  "found_by": "the king, while running this beat's own recommended next step"
}