{
  "elements": 2823,
  "genes": 1034,
  "matrix_input": "encode_rE2G_full/vitessce_cvh/cvh_sci/chr19/chr19.matrix.csv",
  "matrix_text_sha256": "8bedf7547cb4e525055d58ea562c4f99d49aebc2827faf2f46cfd21efd0e135d",
  "clinvar_input": "encode_rE2G_full/vitessce_cvh/cvh_sci/chr19/chr19.clinvar.metadata.csv",
  "clinvar_text_sha256": "5b7da28633d86fdedbd265567f572ddfba3f598eec333a80785e9155497e1d71",
  "clinvar_positive_elements": 973,
  "map": {
    "x": "element midpoint in Mb",
    "y": "log2(1 + ClinVar count) times scale",
    "y_scale": 2.1257775292600454,
    "raw_count_range": [
      0,
      297
    ]
  },
  "landscape": {
    "method": "UMAP",
    "parameters": {
      "n_neighbors": 25,
      "min_dist": 0.25,
      "metric": "cosine",
      "random_state": 0,
      "n_jobs": 1,
      "input": "L2-normalized gene-score profiles"
    },
    "postprocessing": "center both axes and apply one common scale factor; geometry preserved",
    "packages": {
      "numpy": "2.1.3",
      "scikit-learn": "1.6.1",
      "umap-learn": "0.5.7"
    }
  },
  "gene_feature_ids": {
    "LDLR": [
      "LDLR|ENSG00000130164|chr19:11089361"
    ],
    "APOE": [
      "APOE|ENSG00000130203|chr19:44905748"
    ],
    "TM6SF2": [
      "TM6SF2|ENSG00000213996|chr19:19273265"
    ],
    "CYP2A6": []
  },
  "missing_requested_genes": [
    "CYP2A6"
  ],
  "locus_windows": {
    "LDLR": [
      11050000,
      11150000
    ],
    "APOE–APOC": [
      44870000,
      44970000
    ],
    "TM6SF2": [
      19220000,
      19330000
    ],
    "CYP2A6–2B6": [
      40820000,
      41030000
    ]
  },
  "set_sizes": {
    "Gosling columns": {
      "LDLR locus": 13,
      "APOE–APOC locus": 18,
      "TM6SF2 locus": 4,
      "CYP2A6–2B6 locus": 0,
      "LDLR ±1 Mb": 148,
      "APOE–APOC ±1 Mb": 184,
      "TM6SF2 ±1 Mb": 131,
      "CYP2A6–2B6 ±1 Mb": 97
    },
    "rE2G links (score > 0)": {
      "linked to LDLR": 9,
      "linked to APOE": 10,
      "linked to TM6SF2": 2
    },
    "ClinVar overlap": {
      "With ClinVar overlap": 973,
      "No ClinVar overlap": 1850
    }
  },
  "interpretation": "Exploratory embedding of predicted target-link profiles, not expression, physical distance, or evidence of causal regulation."
}