The KMT2A exon-11 CTCF anchor, placed in its population: baseline strength 4.92x (91.7th percentile of 12,443 RPE anchors), KDM3B-depletion ratio 0.396x, rank 58 of 1,625 strength-matched anchors - a strong, strongly-responding anchor at the edge of a continuum, not an outlier

[
  2.509,
  14.056
]

{
  "matched_S_within_10pct": {
    "n": 1625,
    "rank": 58,
    "percentile": 0.0357,
    "matched_median": 0.633
  },
  "nearest_500_in_S": {
    "n": 500,
    "rank": 22,
    "percentile": 0.044,
    "matched_median": 0.622
  },
  "strength_decile_10": {
    "n": 1245,
    "rank": 61,
    "percentile": 0.049,
    "matched_median": 0.615
  },
  "all_anchors": {
    "n": 12443,
    "rank": 258,
    "percentile": 0.0207,
    "median": 0.696
  },
  "pre_declared_split_replicate_control": {
    "n": 185,
    "rank": 59,
    "percentile": 0.319,
    "ratio": 0.586,
    "matched_median": 0.685
  }
}

{
  "GSM6431023": 9.243,
  "GSM6431025": 4.688
}

{
  "GSM6431019": 1.85,
  "GSM6431021": 2.339
}

[
  0.2,
  0.253,
  0.395,
  0.499
]

{
  "hg19": "chr11:8,241,000",
  "grch38": "chr11:8,370,285",
  "strength": 4.954,
  "ratio": 0.281,
  "both_reps_consistent": true,
  "note": "a near-identical baseline strength on the same chromosome with a LARGER CTCF loss, and no association with any fragile site"
}

{
  "why_this_is_here": "this entry reports the Ensembl patch-mapping set as inverted against registry row 168 and correctly flagged it as a single unrepeated live query. The king re-measured, and got a third answer.",
  "the_kings_measurement_2026_09_22": {
    "2 bp DCAL cut point (width 2)": "1 mapping, chromosome 11 only",
    "canonical exon 11 (width 147)": "2 mappings, chromosome 11 + HG122_PATCH",
    "1,048 bp element (width 1048)": "2 mappings, chromosome 11 + HG122_PATCH",
    "CTCF summit +/-250 (width 501)": "2 mappings, chromosome 11 + HG122_PATCH",
    "BCR core (width 7466)": "2 mappings, chromosome 11 + HG122_PATCH",
    "gene span (width 90341)": "2 mappings, chromosome 11 + HG122_PATCH",
    "offset": "exactly 129,285 bp, CONSTANT across all six intervals"
  },
  "it_reproduces_Q107_not_this_beat": "element 2, exon 2, cut point 1 - Q107's pattern exactly, and the opposite of this beat's element 1 / cut point 2",
  "therefore": "the registry row was NOT dropped. Three observations exist, two agree and one differs, two of them from the same day - which supports this entry's own conclusion that the mapping set is not stable, rather than either party being wrong. The count of mappings is not a reproducible observable; the chromosome-11 mapping and the 129,285 bp offset are, and both are present in all three.",
  "nothing_measured_in_this_beat_is_affected": "this beat filtered on seq_region_name == '11' throughout and re-derived the offset across six widths, so its coordinates are correct under every observed pattern"
}

{
  "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"
}