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data/external/data_sources.yaml

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+access_date: "2026-06-04"
+resources:
+  gasperini_crisprqtl:
+    purpose: "Primary S2T enhancer-gene benchmark."
+    status: "starter_files_downloaded_locally"
+    accession: "GEO:GSE120861"
+    coordinate_assembly: "hg19"
+    assembly_note: "At-scale enhancer coordinates are treated as hg19/GRCh37; chr1 coordinates exceeding GRCh38 length confirm the earlier hg38 assumption was unsafe."
+    publication_url: "https://pubmed.ncbi.nlm.nih.gov/30612741/"
+    geo_supplement_base_url: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120861/suppl/"
+    files:
+      at_scale_pair_table:
+        url: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120861/suppl/GSE120861_gene_gRNAgroup_pair_table.at_scale.txt.gz"
+        local_path: "data/raw/gasperini_gse120861/GSE120861_gene_gRNAgroup_pair_table.at_scale.txt.gz"
+        size_observed: "19M"
+      at_scale_deg_results:
+        url: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120861/suppl/GSE120861_all_deg_results.at_scale.txt.gz"
+        local_path: "data/raw/gasperini_gse120861/GSE120861_all_deg_results.at_scale.txt.gz"
+        size_observed: "36M"
+      at_scale_grna_groups:
+        url: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120861/suppl/GSE120861_grna_groups.at_scale.txt.gz"
+        local_path: "data/raw/gasperini_gse120861/GSE120861_grna_groups.at_scale.txt.gz"
+        size_observed: "128K"
+    license_or_terms: "Public GEO supplementary files; confirm redistribution policy before committing derived data."
+  arc_virtual_cell_challenge:
+    purpose: "Primary T2S gene perturbation response benchmark."
+    status: "manifested_not_downloaded_signature_builder_ready"
+    url: "https://github.com/ArcInstitute/arc-virtual-cell-atlas/blob/main/virtual-cell-challenge/README.md"
+    data_host: "Google Marketplace bucket"
+    bucket: "gs://arc-institute-virtual-cell-atlas/virtual-cell-challenge/"
+    coordinate_assembly: "not_applicable_single_cell_expression"
+    cell_context: "H1 hESC"
+    modality: "CRISPRi"
+    statistics:
+      cells: "~300,000"
+      target_genes: 300
+    files:
+      training_h5ad:
+        url: "gs://arc-institute-virtual-cell-atlas/virtual-cell-challenge/2025/train/adata_Training.h5ad"
+        local_path: "data/raw/vcc/2025/train/adata_Training.h5ad"
+      training_perturbation_counts:
+        url: "gs://arc-institute-virtual-cell-atlas/virtual-cell-challenge/2025/train/pert_counts_Training.csv"
+        local_path: "data/raw/vcc/2025/train/pert_counts_Training.csv"
+    derived_outputs:
+      perturbation_signatures:
+        local_path: "data/processed/t2s/vcc_2025/perturbation_signatures.h5ad"
+        status: "builder_ready_pending_raw_download"
+    license_or_terms: "Follow Arc VCC and Google Marketplace dataset terms before downloading or redistributing derived signatures."
+  encode_ccre_screen:
+    purpose: "Regulatory annotations."
+    status: "PLS_and_ELS_lifted_to_hg19_and_annotated_gasperini"
+    url: "https://screen.wenglab.org/downloads"
+    version: "SCREEN Registry V4, Human GRCh38/hg38"
+    coordinate_assembly: "hg38"
+    assembly_note: "Do not use directly with the hg19 Gasperini benchmark. Use hg19 cCREs or liftOver with QC."
+    liftover:
+      target_assembly: "hg19"
+      config: "configs/ccre_liftover.yaml"
+      chain_url: "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz"
+      local_chain_path: "data/raw/ucsc_liftover/hg38ToHg19.over.chain.gz"
+      bed_plus: 4
+      status: "complete"
+      qc_yaml: "data/interim/screen_v4_liftover/hg19/liftover_qc.yaml"
+      lifted_records:
+        promoter_like:
+          input_records: 47532
+          lifted_records: 47396
+          lifted_fraction: 0.9971387696709585
+        enhancer_like:
+          input_records: 1718669
+          lifted_records: 1715351
+          lifted_fraction: 0.9980694362905248
+    derived_outputs:
+      gasperini_region_annotation:
+        qc_yaml: "data/processed/s2t/gasperini_gse120861/ccre_annotation_qc.yaml"
+        regions_with_ccre: 5810
+        regions_total: 6143
+    files:
+      promoter_like:
+        url: "https://downloads.wenglab.org/Registry-V4/GRCh38-cCREs.PLS.bed"
+        local_path: "data/raw/screen_v4/GRCh38-cCREs.PLS.bed"
+      enhancer_like:
+        url: "https://downloads.wenglab.org/Registry-V4/GRCh38-cCREs.ELS.bed"
+        local_path: "data/raw/screen_v4/GRCh38-cCREs.ELS.bed"
+    license_or_terms: "SCREEN download page requests citation of Moore...Weng (2026) Nature; confirm redistribution policy before committing derived annotations."
+  abc_maps:
+    purpose: "Enhancer-gene contact/activity prior."
+    status: "K562_filtered_predictions_downloaded_locally"
+    url: "https://www.engreitzlab.org/resources/"
+    coordinate_assembly: "hg19"
+    assembly_note: "Local K562 filtered file has chr1 intervals beyond GRCh38 length and aligns with hg19-coordinate Gasperini regions."
+    source_file:
+      url: "https://mitra.stanford.edu/engreitz/oak/public/Nasser2021/AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz"
+      size_observed: "324M"
+    local_filtered_file: "data/raw/abc_nasser2021/K562_AllPredictions.AvgHiC.ABC0.015.minus150.ForABCPaperV3.txt.gz"
+    filter: "header plus rows matching K562; observed CellType is K562-Roadmap"
+    license_or_terms: "Public Engreitz Lab resource; confirm redistribution policy before committing derived ABC scores."
+  encode_re2g:
+    purpose: "No-training external S2T field-model comparison."
+    status: "thresholded_k562_files_downloaded_lifted_and_scored"
+    url: "https://www.encodeproject.org/"
+    model_repo: "https://github.com/EngreitzLab/ENCODE_rE2G"
+    portal: "https://e2g.stanford.edu/"
+    coordinate_assembly: "GRCh38"
+    assembly_note: "Released ENCODE-rE2G files are GRCh38 and must be lifted to hg19 before joining to Gasperini."
+    config: "configs/external_e2g_sources.yaml"
+    liftover:
+      target_assembly: "hg19"
+      chain_url: "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz"
+      local_chain_path: "data/raw/ucsc_liftover/hg38ToHg19.over.chain.gz"
+      bed_plus: 3
+      qc_yaml: "data/external/external_e2g_liftover_qc.yaml"
+    files:
+      dnase_eot_thresholded:
+        accession: "ENCFF976OKL"
+        url: "https://www.encodeproject.org/files/ENCFF976OKL/"
+        download_url: "https://www.encodeproject.org/files/ENCFF976OKL/@@download/ENCFF976OKL.bed.gz"
+        local_path: "data/raw/external_e2g/encode_re2g/ENCFF976OKL.bed.gz"
+        lifted_path: "data/interim/external_e2g/encode_re2g/ENCFF976OKL.hg19.bed"
+        output_type: "thresholded element gene links"
+        md5sum: "1989f02e1ed38c3831fca8abdfcf3d01"
+      extended_thresholded:
+        accession: "ENCFF269DKY"
+        url: "https://www.encodeproject.org/files/ENCFF269DKY/"
+        download_url: "https://www.encodeproject.org/files/ENCFF269DKY/@@download/ENCFF269DKY.bed.gz"
+        local_path: "data/raw/external_e2g/encode_re2g/ENCFF269DKY.bed.gz"
+        lifted_path: "data/interim/external_e2g/encode_re2g/ENCFF269DKY.hg19.bed"
+        output_type: "thresholded element gene links"
+        md5sum: "c358ee5b33b4c03b2bef5ccf83e93c70"
+      dnase_eot_full:
+        accession: "ENCFF970QAX"
+        url: "https://www.encodeproject.org/files/ENCFF970QAX/"
+        download_url: "https://www.encodeproject.org/files/ENCFF970QAX/@@download/ENCFF970QAX.bed.gz"
+        local_path: "data/raw/external_e2g/encode_re2g/ENCFF970QAX.bed.gz"
+        lifted_path: "data/interim/external_e2g/encode_re2g/ENCFF970QAX.hg19.bed"
+        output_type: "element gene links"
+        md5sum: "935d4418891babd748cd74dc074cf73f"
+        status: "downloaded_lifted_scored"
+      extended_full:
+        accession: "ENCFF950FTI"
+        url: "https://www.encodeproject.org/files/ENCFF950FTI/"
+        download_url: "https://www.encodeproject.org/files/ENCFF950FTI/@@download/ENCFF950FTI.bed.gz"
+        local_path: "data/raw/external_e2g/encode_re2g/ENCFF950FTI.bed.gz"
+        lifted_path: "data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed"
+        output_type: "element gene links"
+        md5sum: "fd6affb3db931196ecd074e2ff46fc5f"
+        status: "downloaded_lifted_scored"
+    license_or_terms: "Released ENCODE files; cite ENCODE and ENCODE-rE2G. Use as external no-training comparisons unless terms are reviewed for training use."
+  jaspar:
+    purpose: "TF motif features and explanations."
+    status: "downloaded_locally_pilot_and_k562_erythroid_panel_scanned"
+    url: "https://jaspar.elixir.no/downloads"
+    release: "2026"
+    recommended_collection: "JASPAR CORE vertebrates non-redundant PFM"
+    pfm_url: "https://jaspar.elixir.no/download/data/2026/CORE/JASPAR2026_CORE_vertebrates_non-redundant_pfms_jaspar.txt"
+    local_pfm: "data/raw/jaspar/JASPAR2026_CORE_vertebrates_non-redundant_pfms_jaspar.txt"
+    sha256: "4005b5449ba07d9b58495f51143186e7e3959efd0ad670770fbddf57bf941e8f"
+    size_bytes: 336314
+    derived_panels:
+      k562_erythroid_starter:
+        config: "configs/motif_panels/k562_erythroid.yaml"
+        n_motifs: 37
+        output: "data/processed/s2t/gasperini_gse120861/sequence_features.jaspar2026_k562_erythroid.parquet"
+        feature_rows: 454582
+    license_or_terms: "Open-access database; cite exact release and collection used."
+  ucsc_sequence_api:
+    purpose: "Lightweight hg19/hg38 region sequence extraction before motif scanning."
+    status: "used_for_gasperini_hg19_region_sequences"
+    url: "https://api.genome.ucsc.edu/getData/sequence"
+    local_cache_dir: "data/interim/ucsc_sequences"
+    license_or_terms: "UCSC Genome Browser API; cite UCSC Genome Browser where used."
+  alphagenome:
+    purpose: "No-training oracle/comparison only unless permission changes."
+    status: "optional_oracle"
+    url: "https://www.alphagenomedocs.com/index.html"
+    license_or_terms: "Do not train on API outputs under current conservative project rule."

data/external/external_e2g_liftover_qc.yaml

@@ -0,0 +1,43 @@
+source_config: configs/external_e2g_sources.yaml
+source_assembly: GRCh38
+target_assembly: hg19
+chain_local_path: data/raw/ucsc_liftover/hg38ToHg19.over.chain.gz
+min_match: 0.95
+bed_plus: 3
+files:
+- source_name: encode_re2g_k562_dnase_eot_thresholded
+  accession: ENCFF976OKL
+  input_path: data/raw/external_e2g/encode_re2g/ENCFF976OKL.bed.gz
+  output_path: data/interim/external_e2g/encode_re2g/ENCFF976OKL.hg19.bed
+  unmapped_path: data/interim/external_e2g/encode_re2g/ENCFF976OKL.hg19.bed.unmapped
+  input_records: 87489
+  lifted_records: 87370
+  unmapped_records: 119
+  lifted_fraction: 0.9986398290070752
+- source_name: encode_re2g_k562_extended_thresholded
+  accession: ENCFF269DKY
+  input_path: data/raw/external_e2g/encode_re2g/ENCFF269DKY.bed.gz
+  output_path: data/interim/external_e2g/encode_re2g/ENCFF269DKY.hg19.bed
+  unmapped_path: data/interim/external_e2g/encode_re2g/ENCFF269DKY.hg19.bed.unmapped
+  input_records: 154122
+  lifted_records: 153912
+  unmapped_records: 210
+  lifted_fraction: 0.9986374430645852
+- source_name: encode_re2g_k562_dnase_eot_full
+  accession: ENCFF970QAX
+  input_path: data/raw/external_e2g/encode_re2g/ENCFF970QAX.bed.gz
+  output_path: data/interim/external_e2g/encode_re2g/ENCFF970QAX.hg19.bed
+  unmapped_path: data/interim/external_e2g/encode_re2g/ENCFF970QAX.hg19.bed.unmapped
+  input_records: 10490107
+  lifted_records: 10470176
+  unmapped_records: 19931
+  lifted_fraction: 0.9981000193801646
+- source_name: encode_re2g_k562_extended_full
+  accession: ENCFF950FTI
+  input_path: data/raw/external_e2g/encode_re2g/ENCFF950FTI.bed.gz
+  output_path: data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed
+  unmapped_path: data/interim/external_e2g/encode_re2g/ENCFF950FTI.hg19.bed.unmapped
+  input_records: 10456392
+  lifted_records: 10436369
+  unmapped_records: 20023
+  lifted_fraction: 0.9980850947439613

data/external/k562_contact_feature_plan.yaml

@@ -0,0 +1,39 @@
+source_audit: data/external/k562_molecular_sources_audit.yaml
+target_assembly: hg19
+candidate_contact_sources: 2
+candidate_contact_matrices: 1
+ready_contact_matrices: 0
+plan_records:
+- family: reference_hic
+  accession: ENCFF621AIY
+  assembly: GRCh38
+  file_format: hic
+  output_type: mapping quality thresholded contact matrix
+  status: released
+  file_size: 33783625697
+  md5sum: 71e5dc072beddbdcda11c9016696e142
+  download_url: https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic
+  s3_uri: s3://encode-public/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic
+  local_path: data/raw/k562_molecular/reference_hic/ENCFF621AIY.hic
+  local_exists: false
+  action: requires_assembly_strategy_before_use
+- family: reference_hic
+  accession: ENCFF134PUN
+  assembly: GRCh38
+  file_format: bed
+  output_type: contact domains
+  status: archived
+  file_size: 58070147883
+  md5sum: cd12d922bb71692d98f924c04e72d038
+  download_url: https://www.encodeproject.org/files/ENCFF134PUN/@@download/ENCFF134PUN.bed.gz
+  s3_uri: s3://encode-public/2023/04/12/9c79af08-d830-4e4d-ae35-bae09c98b328/ENCFF134PUN.bed.gz
+  local_path: data/raw/k562_molecular/reference_hic/ENCFF134PUN.bed.gz
+  local_exists: false
+  action: not_a_contact_matrix
+recommended_next_action: 'No assembly-matched local contact matrix is ready. Current
+  ENCODE K562 .hic candidate is GRCh38 while the Gasperini benchmark is treated as
+  hg19. Choose one controlled path: create a GRCh38/liftOver candidate table with
+  QC, or use an hg19-compatible contact source. Then dump sparse pixels and run scripts/build_k562_contact_features.py.'
+example_sparse_build_command: PYTHONPATH=src .venv/bin/python scripts/build_k562_contact_features.py
+  --contacts data/interim/k562_contacts/k562_10kb_pixels.tsv.gz --contact-assembly
+  hg19 --resolution-bp 10000

data/external/k562_contact_liftover_qc.yaml

@@ -0,0 +1,21 @@
+source_assembly: hg19
+target_assembly: hg38
+chain_url: https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
+chain_local_path: data/raw/ucsc_liftover/hg19ToHg38.over.chain.gz
+min_match: 0.95
+input_bed: data/interim/k562_contacts/liftover/gasperini_contact_anchors.hg19.bed
+output_bed: data/interim/k562_contacts/liftover/gasperini_contact_anchors.hg38.bed
+unmapped_bed: data/interim/k562_contacts/liftover/gasperini_contact_anchors.hg38.unmapped.bed
+output_parquet: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
+input_anchor_count: 144200
+lifted_anchor_count: 144154
+unmapped_anchor_count: 21
+lifted_fraction: 0.9996809986130375
+input_counts_by_type:
+  promoter: 138057
+  region: 6143
+lifted_counts_by_type:
+  promoter: 138011
+  region: 6143
+contact_source_accession: ENCFF621AIY
+contact_source_assembly: GRCh38

data/external/k562_hic_candidate_pixel_qc.yaml

@@ -0,0 +1,35 @@
+hic: data/raw/k562_molecular/reference_hic/ENCFF621AIY.hic
+lifted_anchors: data/processed/s2t/gasperini_gse120861/contact/gasperini_contact_anchors.hg38.parquet
+resolution_bp: 10000
+normalization: NONE
+workers: 10
+candidate_pairs: 138057
+lifted_query_pairs: 138011
+unique_lifted_bin_pairs: 91017
+nonzero_pixel_count: 81528
+nonzero_pixel_fraction_of_unique_queries: 0.895744750980586
+chromosomes:
+  chr1: chr1
+  chr10: chr10
+  chr11: chr11
+  chr12: chr12
+  chr13: chr13
+  chr14: chr14
+  chr15: chr15
+  chr16: chr16
+  chr17: chr17
+  chr18: chr18
+  chr19: chr19
+  chr2: chr2
+  chr20: chr20
+  chr21: chr21
+  chr22: chr22
+  chr3: chr3
+  chr4: chr4
+  chr5: chr5
+  chr6: chr6
+  chr7: chr7
+  chr8: chr8
+  chr9: chr9
+  chrX: chrX
+output: data/interim/k562_contacts/ENCFF621AIY.10kb.candidate_pixels.parquet

data/external/k562_molecular_feature_build_plan.yaml

@@ -0,0 +1,42 @@
+source_audit: data/external/k562_molecular_sources_audit.yaml
+assembly: hg19
+candidate_bigwig_sources: 3
+ready_bigwig_sources: 3
+plan_records:
+- family: dnase
+  accession: ENCFF827NRR
+  identifier: null
+  assembly: hg19
+  file_format: bigWig
+  output_type: signal of unique reads
+  status: archived
+  download_url: https://www.encodeproject.org/files/ENCFF827NRR/@@download/ENCFF827NRR.bigWig
+  file_size: 168663469
+  md5sum: c1787835e5e231d7cf2bc3387b2bf97a
+  local_path: data/raw/k562_molecular/dnase/ENCFF827NRR.bigWig
+  local_exists: true
+- family: dnase
+  accession: ENCFF447GZO
+  identifier: null
+  assembly: hg19
+  file_format: bigWig
+  output_type: signal of unique reads
+  status: archived
+  download_url: https://www.encodeproject.org/files/ENCFF447GZO/@@download/ENCFF447GZO.bigWig
+  file_size: 171310286
+  md5sum: 6009f78f2bc6b21bfc03a9d5e78c6513
+  local_path: data/raw/k562_molecular/dnase/ENCFF447GZO.bigWig
+  local_exists: true
+- family: h3k27ac
+  accession: null
+  identifier: https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegMarkH3k27ac/wgEncodeBroadHistoneK562H3k27acStdSig.bigWig
+  assembly: hg19
+  file_format: bigWig
+  output_type: null
+  status: null
+  download_url: https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegMarkH3k27ac/wgEncodeBroadHistoneK562H3k27acStdSig.bigWig
+  file_size: 306678205
+  md5sum: null
+  local_path: data/raw/k562_molecular/h3k27ac/wgEncodeBroadHistoneK562H3k27acStdSig.bigWig
+  local_exists: true
+next_action: run without --plan-only to aggregate ready local bigWig files

data/external/k562_molecular_sources_audit.yaml

@@ -0,0 +1,478 @@
+generated_at: '2026-06-08T16:21:37.042878+00:00'
+source_config: configs/k562_molecular_sources.yaml
+assembly_target: hg19
+record_count: 29
+ok_count: 20
+failed_count: 0
+manual_count: 9
+records:
+- family: cage
+  provider: FANTOM5
+  biosample: K562
+  assay: CAGE
+  identifier: CNhs11250
+  usage: promoter activity and target-gene expression/power covariates
+  validation_status: manual_required
+- family: cage
+  provider: FANTOM5
+  biosample: K562
+  assay: CAGE
+  identifier: CNhs12334
+  usage: promoter activity and target-gene expression/power covariates
+  validation_status: manual_required
+- family: cage
+  provider: FANTOM5
+  biosample: K562
+  assay: CAGE
+  identifier: CNhs12335
+  usage: promoter activity and target-gene expression/power covariates
+  validation_status: manual_required
+- family: cage
+  provider: FANTOM5
+  biosample: K562
+  assay: CAGE
+  identifier: CNhs12336
+  usage: promoter activity and target-gene expression/power covariates
+  validation_status: manual_required
+- family: cage
+  provider: FANTOM5
+  biosample: K562
+  assay: CAGE
+  identifier: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562.CNhs11250.10454-106G4.hg19.ctss.bed.gz
+  validation_status: url_ok
+  download_url: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562.CNhs11250.10454-106G4.hg19.ctss.bed.gz
+  assembly: hg19
+  file_format: bed
+  content_type: application/x-gzip
+  file_size: 14817958
+  last_modified: Wed, 29 Jun 2011 10:40:06 GMT
+- family: cage
+  provider: FANTOM5
+  biosample: K562
+  assay: CAGE
+  identifier: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep1.CNhs12334.10824-111C5.hg19.ctss.bed.gz
+  validation_status: url_ok
+  download_url: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep1.CNhs12334.10824-111C5.hg19.ctss.bed.gz
+  assembly: hg19
+  file_format: bed
+  content_type: application/x-gzip
+  file_size: 9107710
+  last_modified: Wed, 29 Jun 2011 12:53:42 GMT
+- family: cage
+  provider: FANTOM5
+  biosample: K562
+  assay: CAGE
+  identifier: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep2.CNhs12335.10825-111C6.hg19.ctss.bed.gz
+  validation_status: url_ok
+  download_url: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep2.CNhs12335.10825-111C6.hg19.ctss.bed.gz
+  assembly: hg19
+  file_format: bed
+  content_type: application/x-gzip
+  file_size: 10122187
+  last_modified: Wed, 29 Jun 2011 12:54:25 GMT
+- family: cage
+  provider: FANTOM5
+  biosample: K562
+  assay: CAGE
+  identifier: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep3.CNhs12336.10826-111C7.hg19.ctss.bed.gz
+  validation_status: url_ok
+  download_url: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep3.CNhs12336.10826-111C7.hg19.ctss.bed.gz
+  assembly: hg19
+  file_format: bed
+  content_type: application/x-gzip
+  file_size: 11214315
+  last_modified: Wed, 29 Jun 2011 12:55:15 GMT
+- family: ctcf_cohesin
+  provider: ENCODE
+  biosample: K562
+  assay:
+  - CTCF ChIP-seq
+  - RAD21 ChIP-seq
+  - SMC1A/SMC3 ChIP-seq
+  accession: ENCFF168IFW
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF168IFW/
+  status: released
+  assembly: GRCh38
+  file_format: bigWig
+  output_type: signal p-value
+  file_size: 427316411
+  md5sum: 8f9feb5f030d25a4f2623e0404d63357
+  biological_replicates:
+  - 1
+  - 2
+  technical_replicates:
+  - '1_1'
+  - '2_1'
+  dataset: /experiments/ENCSR000DWE/
+  download_url: https://www.encodeproject.org/files/ENCFF168IFW/@@download/ENCFF168IFW.bigWig
+  s3_uri: s3://encode-public/2020/09/25/5f56d601-0bb6-4781-a8a0-76f3ad7d7d52/ENCFF168IFW.bigWig
+- family: ctcf_cohesin
+  provider: ENCODE
+  biosample: K562
+  assay:
+  - CTCF ChIP-seq
+  - RAD21 ChIP-seq
+  - SMC1A/SMC3 ChIP-seq
+  accession: ENCFF736NYC
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF736NYC/
+  status: released
+  assembly: GRCh38
+  file_format: bed
+  output_type: IDR thresholded peaks
+  file_size: 724170
+  md5sum: 606e423b6ab856b7a61767838d21dbf8
+  biological_replicates:
+  - 1
+  - 2
+  technical_replicates:
+  - '1_1'
+  - '2_1'
+  dataset: /experiments/ENCSR000DWE/
+  download_url: https://www.encodeproject.org/files/ENCFF736NYC/@@download/ENCFF736NYC.bed.gz
+  s3_uri: s3://encode-public/2020/09/25/a988bfd0-11ca-4abf-8662-29f30dc09772/ENCFF736NYC.bed.gz
+- family: ctcf_cohesin
+  provider: ENCODE
+  biosample: K562
+  assay:
+  - CTCF ChIP-seq
+  - RAD21 ChIP-seq
+  - SMC1A/SMC3 ChIP-seq
+  accession: ENCFF330SHG
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF330SHG/
+  status: released
+  assembly: GRCh38
+  file_format: bed
+  output_type: IDR thresholded peaks
+  file_size: 935586
+  md5sum: 356a9862fda97a5f8c636305ebd360c0
+  biological_replicates:
+  - 1
+  - 2
+  technical_replicates:
+  - '1_1'
+  - '2_1'
+  dataset: /experiments/ENCSR942XQI/
+  download_url: https://www.encodeproject.org/files/ENCFF330SHG/@@download/ENCFF330SHG.bed.gz
+  s3_uri: s3://encode-public/2022/08/24/f8806f91-014f-4244-9dd3-7d178df670ed/ENCFF330SHG.bed.gz
+- family: ctcf_cohesin
+  provider: ENCODE
+  biosample: K562
+  assay:
+  - CTCF ChIP-seq
+  - RAD21 ChIP-seq
+  - SMC1A/SMC3 ChIP-seq
+  accession: ENCFF355MNE
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF355MNE/
+  status: released
+  assembly: GRCh38
+  file_format: bed
+  output_type: conservative IDR thresholded peaks
+  file_size: 767024
+  md5sum: eb5e6feb3e8862f026ba5b27e43eaec5
+  biological_replicates:
+  - 1
+  - 2
+  technical_replicates:
+  - '1_1'
+  - '2_1'
+  dataset: /experiments/ENCSR388QZF/
+  download_url: https://www.encodeproject.org/files/ENCFF355MNE/@@download/ENCFF355MNE.bed.gz
+  s3_uri: s3://encode-public/2020/11/27/93ca2939-f77a-41d7-a4a4-ffbad350dd95/ENCFF355MNE.bed.gz
+- family: ctcf_cohesin
+  provider: ENCODE
+  biosample: K562
+  assay:
+  - CTCF ChIP-seq
+  - RAD21 ChIP-seq
+  - SMC1A/SMC3 ChIP-seq
+  identifier: ENCODE search for K562 released bigWig/peak files
+  usage: boundary, loop, and TAD-context features after activity/contact features
+    are stable
+  validation_status: manual_required
+- family: dnase
+  provider: ENCODE
+  biosample: K562
+  assay: DNase-seq
+  accession: ENCFF827NRR
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF827NRR/
+  status: archived
+  assembly: hg19
+  file_format: bigWig
+  output_type: signal of unique reads
+  file_size: 168663469
+  md5sum: c1787835e5e231d7cf2bc3387b2bf97a
+  biological_replicates:
+  - 1
+  technical_replicates:
+  - '1_1'
+  dataset: /experiments/ENCSR101TGA/
+  download_url: https://www.encodeproject.org/files/ENCFF827NRR/@@download/ENCFF827NRR.bigWig
+  s3_uri: s3://encode-public/2016/05/11/1367eb79-10ef-4fa0-ae79-66024926f6e5/ENCFF827NRR.bigWig
+- family: dnase
+  provider: ENCODE
+  biosample: K562
+  assay: DNase-seq
+  accession: ENCFF425WDA
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF425WDA/
+  status: released
+  assembly: GRCh38
+  file_format: bam
+  output_type: alignments
+  file_size: 798775645
+  md5sum: 55077c1a250db3ed78d9c937d92dc86c
+  biological_replicates:
+  - 2
+  technical_replicates:
+  - '2_1'
+  dataset: /experiments/ENCSR000EOT/
+  download_url: https://www.encodeproject.org/files/ENCFF425WDA/@@download/ENCFF425WDA.bam
+  s3_uri: s3://encode-public/2020/11/18/c0cf66b0-28e0-44d3-9df1-0dc3789a1cb7/ENCFF425WDA.bam
+- family: dnase
+  provider: ENCODE
+  biosample: K562
+  assay: DNase-seq
+  accession: ENCFF205FNC
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF205FNC/
+  status: released
+  assembly: GRCh38
+  file_format: bam
+  output_type: alignments
+  file_size: 11870480765
+  md5sum: 6b180efe8b376ebc57ae30e8c6bf37fb
+  biological_replicates:
+  - 1
+  technical_replicates:
+  - '1_1'
+  - '1_2'
+  dataset: /experiments/ENCSR000EOT/
+  download_url: https://www.encodeproject.org/files/ENCFF205FNC/@@download/ENCFF205FNC.bam
+  s3_uri: s3://encode-public/2020/11/18/62e44159-c267-4b15-a8ee-3d100fbf4418/ENCFF205FNC.bam
+- family: dnase
+  provider: ENCODE
+  biosample: K562
+  assay: DNase-seq
+  accession: ENCFF447GZO
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF447GZO/
+  status: archived
+  assembly: hg19
+  file_format: bigWig
+  output_type: signal of unique reads
+  file_size: 171310286
+  md5sum: 6009f78f2bc6b21bfc03a9d5e78c6513
+  biological_replicates:
+  - 1
+  technical_replicates:
+  - '1_1'
+  dataset: /experiments/ENCSR945ENZ/
+  download_url: https://www.encodeproject.org/files/ENCFF447GZO/@@download/ENCFF447GZO.bigWig
+  s3_uri: s3://encode-public/2016/05/11/86462f8e-6200-4c6e-9609-5eea74661242/ENCFF447GZO.bigWig
+- family: external_e2g_predictions
+  provider:
+  - ABC
+  - ENCODE-rE2G
+  - gABC
+  biosample: null
+  assay: null
+  identifier: ABC
+  usage: external-score comparison on exact Seq2State candidates before retraining
+  validation_status: manual_required
+- family: external_e2g_predictions
+  provider:
+  - ABC
+  - ENCODE-rE2G
+  - gABC
+  biosample: null
+  assay: null
+  identifier: ENCODE-rE2G
+  usage: external-score comparison on exact Seq2State candidates before retraining
+  validation_status: manual_required
+- family: external_e2g_predictions
+  provider:
+  - ABC
+  - ENCODE-rE2G
+  - gABC
+  biosample: null
+  assay: null
+  identifier: gABC
+  usage: external-score comparison on exact Seq2State candidates before retraining
+  validation_status: manual_required
+- family: h3k27ac
+  provider: ENCODE
+  biosample: K562
+  assay: H3K27ac ChIP-seq
+  accession: ENCFF779QTH
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF779QTH/
+  status: released
+  assembly: GRCh38
+  file_format: bigWig
+  output_type: fold change over control
+  file_size: 236381149
+  md5sum: 81aaf56e59eaa1c9742b5e0c8216860f
+  biological_replicates:
+  - 1
+  - 2
+  technical_replicates:
+  - '1_1'
+  - '2_1'
+  dataset: /experiments/ENCSR000AKP/
+  download_url: https://www.encodeproject.org/files/ENCFF779QTH/@@download/ENCFF779QTH.bigWig
+  s3_uri: s3://encode-public/2016/08/12/2e25c3ae-0b4a-4155-8750-d959da5dbb5c/ENCFF779QTH.bigWig
+- family: h3k27ac
+  provider: ENCODE
+  biosample: K562
+  assay: H3K27ac ChIP-seq
+  accession: ENCFF544LXB
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF544LXB/
+  status: released
+  assembly: GRCh38
+  file_format: bed
+  output_type: pseudoreplicated peaks
+  file_size: 1455796
+  md5sum: 81a2d09ef690a3317f6b0e793690cfdc
+  biological_replicates:
+  - 1
+  - 2
+  - 3
+  technical_replicates:
+  - '1_1'
+  - '2_1'
+  - '3_1'
+  - '3_2'
+  dataset: /experiments/ENCSR000AKP/
+  download_url: https://www.encodeproject.org/files/ENCFF544LXB/@@download/ENCFF544LXB.bed.gz
+  s3_uri: s3://encode-public/2022/06/14/77871d7d-ef0b-40da-8537-48dfd391bbdf/ENCFF544LXB.bed.gz
+- family: h3k27ac
+  provider: ENCODE
+  biosample: K562
+  assay: H3K27ac ChIP-seq
+  accession: ENCFF600THN
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF600THN/
+  status: released
+  assembly: GRCh38
+  file_format: bam
+  output_type: alignments
+  file_size: 465061663
+  md5sum: d0cb34fd6b9f4b64fee14031d5f130e1
+  biological_replicates:
+  - 1
+  technical_replicates:
+  - '1_1'
+  dataset: /experiments/ENCSR000AKP/
+  download_url: https://www.encodeproject.org/files/ENCFF600THN/@@download/ENCFF600THN.bam
+  s3_uri: s3://encode-public/2022/06/14/03e349f5-48f1-474f-812e-a1830ee6df4f/ENCFF600THN.bam
+- family: h3k27ac
+  provider: ENCODE
+  biosample: K562
+  assay: H3K27ac ChIP-seq
+  accession: ENCFF232RQF
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF232RQF/
+  status: released
+  assembly: GRCh38
+  file_format: bam
+  output_type: alignments
+  file_size: 2455019320
+  md5sum: 60129abdf21c0cb86ee3b918e62e172c
+  biological_replicates:
+  - 3
+  technical_replicates:
+  - '3_1'
+  - '3_2'
+  dataset: /experiments/ENCSR000AKP/
+  download_url: https://www.encodeproject.org/files/ENCFF232RQF/@@download/ENCFF232RQF.bam
+  s3_uri: s3://encode-public/2022/06/14/f84f4ebb-3154-4a2b-8106-23360a30bd47/ENCFF232RQF.bam
+- family: h3k27ac
+  provider: ENCODE
+  biosample: K562
+  assay: H3K27ac ChIP-seq
+  accession: ENCFF704LGA
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF704LGA/
+  status: released
+  assembly: GRCh38
+  file_format: bam
+  output_type: alignments
+  file_size: 226787968
+  md5sum: f58b860384aaeceebbb64f77df1dc837
+  biological_replicates:
+  - 2
+  technical_replicates:
+  - '2_1'
+  dataset: /experiments/ENCSR000AKP/
+  download_url: https://www.encodeproject.org/files/ENCFF704LGA/@@download/ENCFF704LGA.bam
+  s3_uri: s3://encode-public/2022/06/14/47636cb3-e39f-4554-a8aa-fa7c22f3fc93/ENCFF704LGA.bam
+- family: h3k27ac
+  provider: ENCODE
+  biosample: K562
+  assay: H3K27ac ChIP-seq
+  identifier: https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegMarkH3k27ac/wgEncodeBroadHistoneK562H3k27acStdSig.bigWig
+  validation_status: url_ok
+  download_url: https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegMarkH3k27ac/wgEncodeBroadHistoneK562H3k27acStdSig.bigWig
+  assembly: hg19
+  file_format: bigWig
+  content_type: null
+  file_size: 306678205
+  last_modified: Fri, 28 Jan 2011 05:18:18 GMT
+- family: reference_hic
+  provider: ENCODE
+  biosample: reference or K562-compatible
+  assay: Hi-C
+  accession: ENCFF621AIY
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF621AIY/
+  status: released
+  assembly: GRCh38
+  file_format: hic
+  output_type: mapping quality thresholded contact matrix
+  file_size: 33783625697
+  md5sum: 71e5dc072beddbdcda11c9016696e142
+  biological_replicates:
+  - 1
+  - 2
+  technical_replicates:
+  - '1_1'
+  - '1_2'
+  - '2_1'
+  - '2_2'
+  - '2_3'
+  - '2_5'
+  - '2_6'
+  dataset: /experiments/ENCSR479XDG/
+  download_url: https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic
+  s3_uri: s3://encode-public/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic
+- family: reference_hic
+  provider: ENCODE
+  biosample: reference or K562-compatible
+  assay: Hi-C
+  accession: ENCFF134PUN
+  validation_status: ok
+  api_url: https://www.encodeproject.org/files/ENCFF134PUN/
+  status: archived
+  assembly: GRCh38
+  file_format: bed
+  output_type: contact domains
+  file_size: 58070147883
+  md5sum: cd12d922bb71692d98f924c04e72d038
+  biological_replicates: []
+  technical_replicates: []
+  dataset: /annotations/ENCSR382HAW/
+  download_url: https://www.encodeproject.org/files/ENCFF134PUN/@@download/ENCFF134PUN.bed.gz
+  s3_uri: s3://encode-public/2023/04/12/9c79af08-d830-4e4d-ae35-bae09c98b328/ENCFF134PUN.bed.gz
+- family: rna_expression
+  provider: Roadmap Epigenomics
+  biosample: K562 mapping to verify
+  assay: RNA expression
+  identifier: 57epigenomes.RPKM.pc.gz
+  usage: target-gene expression and label-power covariates
+  validation_status: manual_required

data/interim/k562_contacts/liftover/gasperini_contact_anchors.hg38.unmapped.bed

@@ -0,0 +1,42 @@
+#Deleted in new
+chr1	13052997	13052998	contact_anchor_10353
+#Deleted in new
+chr1	13052997	13052998	contact_anchor_10393
+#Deleted in new
+chr1	13052997	13052998	contact_anchor_10432
+#Deleted in new
+chr1	13052997	13052998	contact_anchor_10471
+#Deleted in new
+chr1	13052997	13052998	contact_anchor_10516
+#Deleted in new
+chr12	147052	147053	contact_anchor_42297
+#Deleted in new
+chr12	147052	147053	contact_anchor_42316
+#Deleted in new
+chr12	147052	147053	contact_anchor_42674
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_129414
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_129491
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_129565
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_129637
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_129707
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_129775
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_129858
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_129910
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_129958
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_130003
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_130038
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_130076
+#Deleted in new
+chr7	100612904	100612905	contact_anchor_130112

data/interim/ucsc_sequences/hg19_chr12_92798618_92799067.txt

@@ -0,0 +1 @@
+GGAACACCATTCTTGATCTGAAGAGACAGTACTTAGAACAAGTATTTCAAAAAAAGAATGCTACCGTTTCCTAGGTTGGTACACTGAGGCTTCTGGGGCTGGAATCTGCTTATTTATGAGATAGATTATGAGAATCATAGGTTTGTAAGGAGCCTTCAGGGTCACCTAGTTCAGCCACTGCTAGGTGAGTTTTCTTCAATAAGAATTTTAAACCTGCCTAAAGTGTTATCTGTGGTATCCACCCGCTTCTTCTGCCTTATCTTTGGTCTCCTTTCTTGTCCTTCTCAACCCCACACAATGTGTCAGCACACACAGTGAAACTCCCTGTCCAAAAGGAGAAAAGGCTAAAGGAATTCACATTGAAACAGTTGTGCTAGGCTTCATCCCAAGAATGTGTGCTGGTGTATGTGTGTGTGTGTGTTTTTAATAACTTTTCAAAAATAGAAAAA

data/interim/ucsc_sequences/hg19_chr13_78052311_78052843.txt

@@ -0,0 +1 @@
+CACTCAGCAAACAACCTACCAATACTGTTGCTTTTGAATGTTCTGTAAGGTCGAATGCCAATGATTTGTGTTTTGTTGTGTTACGGTTGCCCAGCCTCCTTGATCTATTGTAGGCAGGGTTAAATTACAGAGTGAATTGGGGGACTGACCTCATTACATCATCTGTGCTGAATCACTGTCCTACAACTGTCGTCCTGAAGGCTCGGGCCAGACGTGGTAGTGCTGTCTTTCATTAATGTTACATTAATATGATCAAGAAGATACTTTCTTCTCTTGCTTCTACCCCCACCCCCACCCCTCAGGTCTCTCATTTGCTAAACAATCAAATGCTTTCAAAATCCTGCAAAACAGCTTTCATTTTAAGGTTCTGATCAAAGGACTTGCATTGCAACATCCCCAGTATTTTCACTGCCCTCTAGTGGCTGTTTTCAATTACATTTTGTTTTACAAAGAGGATTGTATCCTTGTTTCTTTACCGTGTTGGGTCTCAAATAAAAAGCTCTGTATGGCAAGTCATCTTCTAAGAACGTGA

data/interim/ucsc_sequences/hg19_chr18_20031842_20032485.txt

@@ -0,0 +1 @@
+CCATGGGAGTATTCCCATGGCTCCCATTTTATAGGCGAGGACAGGAAGAAAAAAGAGGGTAAGTGAAAGTTTGCTTGAAGGTCACCCAAAGGGGGAGCCGATAGTCAGACCAGGTCAGCTCTCCTTTTGGCCAAAGTCTCCTGACCGCTGAGATGAAAACAGCGGTGGGCTCCTCCAGGGAGGGTTTGGAGAGCAGAAGCTAAATCAGCCACAGGTTCCTTTTGTGTTGATTGAGTCACAAAGCCTCCAGGAGCTGCCAAGTGGCACAAGATGCTGCACTAGGTTTGGAATAAGAAGGCCCCCAGACCCAGTCTCACCCCCAGCTTGGCTGGGGCACTAAACGATTTTAAAAATAAAACTAGAGAGGCCCTGCGTAAACGGCAGGGGATCCATGTCCACCTGACAGCCCTTGGAGCTAACGCTAAGGGAGGACAGCTTGCAACAAGGGGCACGGGGCCTGAGATAAAGGAAGCGGTCACCTAGAGGGACGGGCCATCTGTCAAGCCAGTTCTTTCCCTCCCCTCCCTTCCCTTCCCCTCCCCTCCCCTCCTTTTCCTTTCTTTTCTTCTTTCCTTTTCTCTTTTCTTTCTTTTCTTTTCTCTTTCTACAGTCTCATTCTGTTTCCCAGGCTGGAGTGCAGTGG

data/interim/ucsc_sequences/hg19_chr1_226189819_226189982.txt

@@ -0,0 +1 @@
+GGGGCTGATCAGTGATTATGGAAAAGAGCCAACTGCTGCTACCTTTCCCACCTCATGACGTCAGGGAAGGCACAGGAAGGCACGTGTGTGGTTGTGACAACTAAATGGTGAGTGGGAGGGGGGCCAGTTCCTCTATTGTCTACATAGTGTGGCCATGCTCCTC

data/interim/ucsc_sequences/hg19_chr20_45989266_45989921.txt

@@ -0,0 +1 @@
+AAAACGTGTCTCTCTTAATATTCCCAGGGTACAGAGAGGATTGGGGTACAGAATCAGGCTGTGGGGAGCCAGGCAGAGTGTCACAGTAACAACACTGGTCTCGAGGGAGAGGAAAGGCTGGCCCCAGCTCCCTTCCCCCAGCACCTTACGAGCTGAGGCCTGGCCTCCCTGAAATGGCTCGCCCGTTCCGCTGGCCTCCAGCCAGGCGAGCAGCAGCAGGAGCGGCCCCACAAGCTGCATCCCGAGATAGCCTGTTCGGCTGCCTACAAAAATAAGCACACTTGCAGTTATCGGCCTCCAGCTACAGCAGGCCTCTCTGACCGTTACGCGAAATGGACAGGATTGAGTCAGGGAAGTGTTTTAAATATCTTGTTTTGTTTTGTTCCTTTCTGGCCAATTAGAACCGAGGCCAACTTCGGGCACGGTGACAGAAGGGCTCACCTTCAGAGCCCGGAGCTGACTGTGTCATGTTACAGCCACAAAGAGGCAGATAGGAGCCTCCCTCCCTTGGAGAAGATGCCTACTAGGAGAGGGGTGTGGGGTTTTTTGGTTTTGTTTTGTTTTTTTACCTCTTTCTAGGAGGGACTGGCAGGATTAGGCAAACGGCGGGAGGGAAAACAAAAAGGGCTAGTGGAAAGGGCAGGGGGTGGATGGT

data/interim/ucsc_sequences/hg19_chr2_32037161_32037791.txt

@@ -0,0 +1 @@
+TGGAAAAAGAAAACCTGAAGTTTAAAGACAGAATCAGAACTGAAAGCAAGAACAGAAGCACTTCCTCTTAGAATCAGACATCCGGACCACACTCCTTGCCCTGACAGAGCGTAGGACATCTAGAAGGTTAGAGGAGAAGTCTGACTGTCATGGGGAGGAAGTTTGCCTAAACCAAGGCTGGTGCCCTCTCTAAAGCAGTTCAAAAGAATTTGAAAACACCAGCTCTGAGCACCCCACATAGCTTGTCAACTCACCCCATGTTATCTCAGTCATGATGACTCAACACTAGAGCCTGGCTTGGCCAGAGCACTGAGGCTACAGCCTTCTGTAAACAAGACCAAGGACACAGGACAGCAAGAAAGAAGACAGACAGGTCACTCTCCTGGCTACTTCTATCCAAACCTGTATATCAAAAGAAGAGAACTTCTCTCATTCACACTGCAGGAGAGGGTACAGGAGCAGAAGGAGTAAAGAGGAGATGGGACTTGGCTTAAGCACTGAAACAAATTGTGTGTCTGCACCCTAAACTGTCAACCCTGGCTATTCTTCAAGGTAAAGAAGAGGGCCCTAAATAATCATTTATGAATCATGTGGTCCAGGCACTCTCCCAGAGATCACTTCTCTCACTCC

data/interim/ucsc_sequences/hg19_chr3_156276205_156276518.txt

@@ -0,0 +1 @@
+GTCAAGTTATGAACCCAAGCAATATGATTCCAGGATGTATGCTCTTAACTACAAATGAATTCTGGTCTCCTCCATGCAGTGGAATCTCTGATTCTGCATGACTGCTCACAAAAGCCCTACACTGAGCAAGCAGCCAAAAGTAGTTTCTTATCTACCAATTATCAGGCACAGTCCTGTCACACTGCAGCTCTCCCTAGTGTATTTTTGGACAGAGAGGATAATAGGCAAACCTTGGTGAGCAGGCCTTGGCTCTCCATACCTGATTCTCTGTCTCAGGGAGTTTGAAAATGAAACCCCAGAAAAAAACAAAACA

data/interim/ucsc_sequences/hg19_chr4_1407726_1410236.txt

@@ -0,0 +1 @@
+GGGGAGGAAGGAGGAGTAAGGGGTTAGAGGCCAGGTACACAGCAGGTGCTCAATAAACGAGTTCGGCACCGTCATCCCGCCCTGCAGGGCCGCTCTGGGTTCGGAGGGCGCGTAGGGAGGGCGGGTCAGGCCGCACAATGAGCTTAATTGAGGTTAATGCCTCCCGCAGCTCCGCGATTATTAAATTATCATCATCACGCGCGTGAATCATAATTAGGAGTTTGAGGAACGCTCCTGCGGAAGCCTTGGAGAGTGATTCTGGCGCCACCGCCTGCTTGGGGCCGCCCGCAGGGAGGGAGTCGGGGTGGGCGCGTGTCCGCGGGAGGGAGTCGGGGTGGGCGCGTGTCCGCGGGAGGGAGTCGGGGTGGGCACGTGTCCGCGGGAGGGAGTCGGGGTGGGCGCGTGTCCGCGGGAGGGAGTCGGGGTGGGCGCGTGTCCGCGGGAGGGAGTCGGGGTGAGCGCGTGTCCGCGGGAGGGGTTAAGGGTGGGCGCGTGTCCGCGGGAGGGGGTAAGGGTGGGCGCCTGTCTGCAGGAGGTGGGTGGAGATGGGCGCGTGTCCGCGGGAGGTGGGTGGGGGTGGGCGCGTGTCCGCGGGAGGGGTTAAGGGTGGGCGCGTGTCCGCGGGAGGGGGTAAGGGTGGGCGCCTGTCTGCAGGAGGTGGGTGGAGATGGGCGCGTGTCCGCGGGAGGTGGGTGGGGGTGGGCGCGTGTCCGCGGGAGGGGTTAAGGGTGGGCGCGTGTCCGCGGGAGGTGGGTGGGGGTGGGCGCGTGTCCGCGGGAGGTGGGTGGGGGTGGGCGCGTGAGCACGGGCTATTGCGCGCTCACGTGGCGCGCCCCCGGCTGAGCCCAAGGCCGGGGTCTCAGAAGGCCCCGCCCACCCCGCAGCGACCCCCCCCCCACGCCCCTCGCACCGCCGAGCCCCTCCCCCAGGGGCCGTTCCCTTCCGGGCCTGCACCGCCCCCGCAGCTGCCCTCCCCCCAGAGCAGCGCCCGCCCCCCTCCTCTCGGCGGTTGGGAGCCGGCCCCGCCCTCGCCCGCTCCCCGCGCCGCCCCTACATTTTCTGATTCTCTGCGACCTTCGCGGATCCCCCCGTCCCCTGCAAAGCCTCGGCCCCTCCCGGCACCCGCAGGACCCCGTGAGTGGCGCGTGGGTGTCCGTCCCGCGCGTCCGACCTGTGATCTCCGAGTGGGTGCGTGCGCCTGAGACCGCGCGGTGTGTCCGAGTGTCCGCATCCACGTGTCCCTACGATCGTGTGCATTGCGGGGCATCCACGCGTGTCCGTGTCCGTGTGTGACCGCACGGTGCATGCCAACCACGGCCTGTGTGAGCGTCCGGGCGTCCGTGGGTTTGTGCGCGTGGATGCGTGTGTTTCTGCTCCTGGCTTGAGCGTGTCCGGGGCCTCTGTCGTGGGCCTGTGGCGGGGCCCCTGGAGTGGGCCCCCTGGTCTCCGGCCGGGCTGCAGTGCCATGTGCGGTGTCTGTGTGCGACTCAGTCCCTCGGCCCTGTCCTTTGGCCCCTCCCCCTCACAGCCTCGTGGGCTTGGCCAAAAGGAGCCCCCCAGAAAAGACGAGGGATGTAGAGTCCAGCGTCCCCAAGGCAAGAGACAAGTCAGTCACCCCCTCCTCTTGAACGGATCCTCCTATCCCACTTCCAGCACTTCAATTCTCCATTTATTTTCCTCTCTGTTGCCGAAACATATTGAAGGGGAGAAAAAGGAAACATTAAGATCCACTGTGAGCTGCGCGGAGGTTTAACGATTTCAAATGAGGCCCGGCTCGGGTGAGGACCTGACAATTCCCCGTCAGGATGGCAGATGACGGCTAAAATTACCCGGAATCAATATTCTCACCGGGTGTCCCGGGCTGATAAGCTCCGCCAAGACAATGTTGACTATTAAAGTCGACAGCTTGAGATATTACACTATTAGTTATGCTATTTTTAATAATCTATAATATTTGGGCTATAATTAATTAATTATACGGGTCAGATAATATCTAGGGCTGGAATGAGGTCTGAAGGACCCATTACGGTGGTAATGAGAAAGGGGAAATCTAATCTGGGGACAGGTGCTGCGAAGGCCTGGGATACTGCTGCCCGCCTCGCTGGCCTCGTCCCCACCAGCAGGCCCAGCATGGCCCAGCTTCCTCGGACGCAGCCAGTGGGCACGTCAGGCAGGGTTGCTTGAGGTGGGGCCCTCAGCGGGCCAGGAGGACTGAGAGGCTGGGGTGGAGGGTGGGACTGAGAGGCTGGGGCGGAGGGCGGAACTGAGAGACTGGGGTGGAGGGCCCGCCCGCCTGTGTTGCTGGCCTGCAGCTGCAGACTTGGCCGGGGGGCGGGGGGGCAGGTGCCCACGTTCTTGGCTCTCTTTTGGGGCCTGGAGGGCCCCTGTCCCCCTCCGGCTTTCCTGTCTTTCTCTGAAGTGAGGGCCTGGCTGGACCATTCCCTGCATGTGTGGAGTCCAGTCCTCACCTCGAGCTCCTCCACCACCACCCCACACTCAGAGACTGAAAC

data/interim/ucsc_sequences/hg19_chr5_177508678_177509350.txt

@@ -0,0 +1 @@
+AAAAAAGTCTTGAGCGTAGCCTCCAGGACAGTTTGTGGTCAGCCTCTGCTCCCTTTCAGCTCCCTCCCCGCCTTCCCAGAAGGGAAGGCTGCCTTGGGCTCCAGGTGGGCCACGCCCCTTCAGACGCAGTGACCTTGCTTTGGTTGTTTTCGCAGTCTGGAAAGTCCTCTTTTAAGTTACAGGTTGCTGAATGTTTTCTCCGTAGAGGAGTTTATTCTCAGTCTGGCCTGGTAGCCCAGGTCAGGGGCCTCTCCTCCCCTGAGGTGTGCAGACAGACAAGTCACCCGGAGGCTCCTGACAAGGACTCTGCTTGACCCAATATTAGTCGGGCCCCTGAGGCTTCTCCTAGACCCATCTGTGTGCTTCCTTATACAATCCAGTTTTAGCAAGAACCCTGCTAGCTCACTGTGGCAGAAACCCCCCACCCTCCATATCTGATCACCCTTGATATCTGGTCAGGCTTCTCCTCCCCATCACCCCTCTGGTGATGTCTGGTCACCCTAGCCTGTCTTCAGCTAGAATCGTGTTAGGTGAGTTTAGCTAGAATCCCCGACCCCTGATGTTGCTCTTAGTAATTCCCCATCCCCTGGCCCCCACCCTGCTCCTTGGCTATCACCCCCCACTCGCCCATGCTGTACTGGGAGTTGAGCCCAGTCTCTCTCCCCAACTGCA

data/interim/ucsc_sequences/hg19_chr6_125624636_125624816.txt

@@ -0,0 +1 @@
+AGAATGTTTGTGAATAGAGGAGGAGGCATTTGAGGTTTAAGGAGTGATATAGTTTGGCTCTGTGACCCCACCCAAATATCATGTCAAACTGTAATCCTCAAAGTTGGAGGAGGGGCCTGGTGGGAGGTGATTGGATCATGGTGGCAGACTTCCCCCTTGCAGTTCTTGTGATAGTGAGTG

data/interim/ucsc_sequences/hg19_chr6_27569353_27570623.txt

@@ -0,0 +1 @@
+TTTCTCTTACATGCGTCCCGTAATAACCTACATCCTGTCCCTTCACTTCACATCCCTTCTCCCATCACCAAAGAAAGAATCAAAGGGGGTCTAGATAAGCGAGGGAGAGGAAGAACGGGGAAACATGGAAAGAAGAAAGGCGGGAGGGGGTGGGGGGAAGTGGTGGTGGTGGTTTGACCTTGAGGAAGGAAACCAGACGATTGTGCAATAATACTCCAGCCTATCGCATACCCTCGCAGAAACCATTAAGATGCTGAAAATAATTATACAGGGAATACGTAAGTCCCACTCACGGGCTTGTTAAGTTAAAATGTGGTCGGAAGCATTGGGGAAAGCTCCTGAAAGGTGGTAGTTGCAAAATGGTTTTGGTAAAATCTACATCTCAAGCCCTTTTCTCCTGTTTTTGTTTGTTTTAGACACGATCTCGCGCTGTCGCCCTGGCTGGAGTGCAGTTGCGCGATCATACAGCTCACTGAAGCTTCGCGCTCCTGGGCTCAAGTGATCAAGCCATTCTCCTACCCAGGTAGCTGGGACTACAGGCGCGCGCCACCAAGCACCGCTCATTTTTTCTATAGACGGGGTGGAACTCCTGGGCTCAAACAATCCTCCCCGCTTAGTCCCCTAATCCTAGTGGTTTTTTGCTTTTTTTTTTTTTTTTTTTTTTCCTCTTGGCTTTTTGAGAGGGAGTCTTGCTTGGTCGCCTGGGCTGGAGTGCAATGGCATGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTTAAGCGATTCTCCTGCCTCAGCCTCTCAAGTAACTGGGATTACGAGCACCCACAACTACTCCCAGCTAATTCTTGTATTTTTAGTAGAAATGGGGTTTCGCCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCACCTGTCTTGGCCTCCCAAAGTGCTGAGATTACAGGTGTAAACCACGGCACCCAGTCCCCCAATCCTAGGATTAAAGGGGCAAAATAGCTGTGTCAGAAGTGGGATTCGAACCCACGCCTCCATGCGGAGACCAGAAGCCCCAAACCTGGGAAGTAGCAACTTGAGTCTGGCGCCTTAGACCACTCGGCCATCCTGACACGCACTGTTACTCCTTAAGTTTCATTATGTAACTCGTAGTCAGCAGACGCTGACTCCGACAAAGGAGGAAAAGACCTCGGATGGGTGGCGTACGCTCCTGGTTTTCACAACGGTATTTATTATTTTGCCCGGTGCTATTCTAAATGATGCTAAACATAGCATCATCAA

data/interim/ucsc_sequences/hg19_chr6_4984915_4985508.txt

@@ -0,0 +1 @@
+ACTGCGCCTGGCCAGTCTTTTCTTTAAAATGGAAGATAGTCTAACATGGTATTAACTGGCAGGTATAGATAGTTTGAAAACATGAGTCAATATGGGATGACTAAAGAGAATTAACAGCAATTTATCTTATTTCCAACTTCAACTGACACCTCCTAAGTTCCTTGTTATATCACTTCCTCTCTGTTGGTGTGCATTCTTACAGATTATAAGAGTAACACACTGTAACAACACCGCCTTCCTGGCTTCCTGCTGGGCTGGTTCCATCAGGTTGAGGGAGGAAGAACCCAGCAGCTGGAAGCTTTCTCAGTCCTTTGTGACAGGACTCCTCAGGATGGTGATATATTGTCAAGGTCCAAGCGGTCCTGGATGCATGAGTCACTGAGCTAGAAACTTCAGGAGAGTCAGCGGCTGGAGACACTGACCTGCCCTCAAGACTTAGAGCCAAGGAGGAGCCTGAAGATAGGGTGGAGAAGCTCCAAGACAAAACGAGCAGGCTGTGTCCTCAGTGTGCAGAGTGCTCCAGAGAAGAGAAAGGCAACTTCTGCTGGGGAATCATGCAGGAGGTGACAACCCCCTGGGGAAGTGATGGGCTG

data/interim/ucsc_sequences/hg19_chr9_135902515_135902941.txt

@@ -0,0 +1 @@
+ATGAGCCACCGCTCCCAGCCAAAGCTACTTTTTAACTGGGTTCCTGATCTTTCTTGGCCTGTCTCTGCTCCCAGCCTTGCCTTACTGCTCCTGCCTCTGACCTCCCGCTTTGGATCTCAGGCAGGACCAAGTCTAATCTCAAAAAGCTTGGTCTGATGCCCTGGGGTTGGTCCCTTGTCTTCCCCTCACACTCAGCCCCTCCTCACTTCCTGTGCACTAAGGGACACTCCTTGTCTGACAAGCCTTGATTTAGTGTCCCTATGACCATGCCCTGACCCGGGGCTCGATTGAAGGCTCAAATAAGACAAGTGGCCTCATTCAGTTGTTCAATAAATACTTCCTGAGCACCTGCTCGGTGCTCAGCCCCATGCAAAGCAGTGGTGACAGTGGGAAGACAGTGGTGAATAAGACAGACATGGTCCCTGT

data/interim/ucsc_sequences/hg38_chr1_1091459_1094313.txt

@@ -0,0 +1 @@
+GGGGGCACCTACCGTGTTCTCCATGGACTTGCTGGCGACTCCCACGAGAAGGCCAGCCAGGAGGGCGAGGTGCCGCAGCGCCATGCCAGGAGCAGATGCGCAGAGCCTGCCACAGGGAGGAGCATGCGGAGCCAAAGAGATGGAGTGGGGCTGAGGCAGGGTGGGTGGGGCCAAATGAAAGTGGGGTCAAGAGATGTTGGGGGGGTGCGGGCCAAGGCAAGGAGGGCAGAGCCAAATGGAGATGGGTGGGGCTGTGGTGGAGGGTGGGGCCAAATGGAAGTGGGCGGGGCTGTGGTGGAGGGTGGGGCCAAATGGAAGTGGGCGGGGCTGTGGCAGGGAGGGTGGGGCCAAATGGAGATGGGGTGGGGCGGGGCCGCGGCAGATGACTGAGTTAAATGGAGATGGGGCAGGGCCGTGGCAGGGGTGCAGGGCCACGACAGGGAAGGTGGAGCCAAATGGAGGTGGGGTGAAAGAGTGAAGGCTTGGGGCCTTTGGAGGCACGGGTGGGGCGAGGTGTAGGCAGGGCCTTACCTGCCCCTCCAGGATGGGGACTACCGACATCAGCCCTTTGCCCGCCTGGGTGTTCAGGGGTTAGCTCTGGGAGCTCATGGGCTCAGCTGAGCCCTGCAGACCCCGGCCCAGTCCTGCAGATGAAGACAGCAGGTGAGGCCGTGGTCACGCGAGGGCAACCCAGGTGGGCCGTGGCCTACGGTGCGGGGTCTGGGTCCGGTCCGGGCCCTCTGTCCACACCCTTGCCGGCCCCTGGCTGTCGAGCAGGGCGTCCTGGAGGGGCTGTCTCCACGAGTGTTTCCCCCGAGCTGGCCTCCTGGCCTCCTGCGGGTGAGAGTGCCTGGGATACAGGCCCTCGCTGGGATACGGGCCCTCGGCCCGGCCTTTGCTCAGGGACCAGGTACGGAGCTCAGTGGCCCAGGCTGCACTTGGTGGACACCGGTCCTCCCGCACAAACCCCCTCTCTCCCCCCTGCACTTCCAGCCACAGGACCTGTTACCATGGCCCTGCCTTCCTAAGGGAGGAAACGCCTGCCAGGCGCACAAATCCTCAAGTGGTGTCACTGCACTGGCTCAGGGGCCTCCCTGGCAAGTTACCCCGAGGGGGGCTGAGGCCCAGCCAGGCCTGTGGGGCTCCTCTTGATGGGCCTAGGCCGGGGTCCTGGGACAAGGGCTGTGAGCAGCAGGGAGACGGAGGCCCTGGAGGACACAGCTCCAGTCTCTGCACAGGGACGGTCCACTCTCCGCACAGGGACGGTCCACTCTGTCACCCATTCCATGCTGGATTCAGGTCATGGCCTCACAAACTGACCAGGCTGCCCAGGTGTGAGCCTGCCGGAGGACTCTGGAAGGTGGGGGTGGTCGGAATGCTTGAGCTCAGGAGTTGGAGACCCACCTGGGCAACACAGCCCGTCTTTACAAAAAGTTTAAAATTAGTCGAGCCTGGTGGTGGGAGCCTGAGGTCCCAGCTACTCAGGAGGCTGAGGTGGGATGATCACCTGAGCCCAGAAGGTGGAGGCTGCAGTGAACGGAGACTGCACTCCAGCCTGTGCAAGGGGAACTCCGTCTCAAAAAAAAAAAGCATGCTCTCCTCTGATTCAGCTCCTCCTCTCTGATGTGAAATCCTTTCAGATGGAACGTGTTGAAGTCACAGACATGCTGCTCGCCCCACCCACAGAGTGCAATCAAGTCTTAGTTTGTCCTTTTGTCCCTTTAACATTTGCCCAGCAGAGACCGTCTTCCCCTGCTCAGTGGAAAACTCCAGACATCACAGACCCTTCTGCTCCCTCTCTGGTTAAAGGGCATCCTGAGGGCCACATTAAGTCACAAAACATCATTTTGATTCAGGAACCAGAAGTCCAAGATTTCAATCAACACTTTCATCTGCTATTTAGTCAACTTCATGGAGATCTACTTTACATACAATAAACCACATCCGTGTAAAGTACACAAGCGGGTGAGTGTGACCACCCCCTTGAAGCTGCCACCACAGCCAGGACGGTGCCCGGTCCCACACAGCTGCCAGCACTCGCTGCGGCCCCCACAAGCCCGGGCTCCCGGCAGCCAGGAGCTGACCAGACTGCAGCTGTATCTTCTAGGGTCTTACACAAAGGGGTTGCACACACTGACCTTTAGATCCTTCCATGTTGTTTTATCCGCACTTTCTTCCTTTCCACAGTCGGAGGATTTTCCACTGTGTTGGCCAAACGTCACCGCCTTTGCCCATCACCTGCCAGTGGGTGCCTGGGCTGCTCCCAGTTCCTGGTGACTGGATGGAGCTGCGGCCAAGGTCCTGGCACATGTCATCATGTGGACATCTGTCTTCATTTCTCTTGGGAGCAGAGTGGCTGGCTCACAGGGAGGTGCACGTTTAACTTTCTAAGGAACTGCAGCCGTCTTCCACAGTGGCTGTGCTGTATACCCTCCCACTGGCGATGTGGGTGCACGCAGGGTGTCCGTGCATGTGCAGGAGTATCTCTGTGTCGTTACAATCTGCATTTCCCTGAAGACTAATGATGGCATCTTTCCATGTGTTTATTAGCCACTTATATATCTTCTTTCTGAAGTGCCTACTCACATCTTCTGCCCATTTTGTTTAATTGGGTGGAGTTGCAACATATACCTTTTTTTTTTTGGCAGGGGTGGGGGGCATAGGGTTTCACTCTGTTGCCCAGGCTGGAGTGCAGTAGTGGGATCGTGGCTCACTGCAGCCTTGACCTCCAGGGCTTACGCGATACTCCTACATCAGCCTCCCGAGTAGCTGAGACTACAGGTGCATGCTGCCATGTTGACCTCCGGGGCTTAAGTGATCCTCCTACCTCAGCCTCTCGAGTAGCTGAGACTAG

results/s2s/s2s_lite_examples/evidence_cards/chr10_3348_top_two.json

@@ -0,0 +1,65 @@
+{
+  "caveats": [
+    "K562 S2T and H1_hESC T2S are not matched biological contexts.",
+    "Composition uses only candidate targets with available T2S perturbation signatures.",
+    "Evidence is deterministic from computed features and does not assert an unsupported mechanism.",
+    "Prediction is model-derived and requires experimental validation.",
+    "Output is for research prioritization, not clinical interpretation."
+  ],
+  "evidence": {
+    "abc_score": 0.230474,
+    "available_t2s_signature": true,
+    "ccre_class": "pELS",
+    "composition_context": "K562 S2T composed with H1_hESC T2S (cross-context)",
+    "composition_method": "weighted_sum_available_t2s_signatures",
+    "context_matched": false,
+    "distance_to_tss": -77398,
+    "is_nearest_gene": 0.0,
+    "n_targets_with_t2s_signature_used": 1,
+    "n_top_targets_considered": 5,
+    "s2t_model": "logistic_distance_abc",
+    "s2t_split_family": "chromosome_fold_3",
+    "signature_weight_sum": 0.569214
+  },
+  "predicted_response": {
+    "score_type": "weighted_mean_delta_expression",
+    "top_response_genes": [
+      {
+        "predicted_delta_expression": -2.73694,
+        "response_gene": "IDE"
+      },
+      {
+        "predicted_delta_expression": -2.263214,
+        "response_gene": "DNMT3B"
+      },
+      {
+        "predicted_delta_expression": -2.172841,
+        "response_gene": "TUBB2B"
+      },
+      {
+        "predicted_delta_expression": -2.014252,
+        "response_gene": "FLNA"
+      },
+      {
+        "predicted_delta_expression": -1.799169,
+        "response_gene": "L1TD1"
+      }
+    ]
+  },
+  "region": {
+    "assembly": "hg19",
+    "cell_context": "K562",
+    "chrom": "chr10",
+    "end": 94334959,
+    "region_id": "chr10.3348_top_two",
+    "start": 94334871
+  },
+  "top_pathways": [],
+  "top_target_gene": {
+    "gene_id": "ENSG00000119912",
+    "gene_symbol": "IDE",
+    "rank": 1,
+    "score": 0.9961354232602443
+  },
+  "uncertainty": "not_calibrated_for_cross_context_composition"
+}

results/s2s/s2s_lite_examples/evidence_cards/chr10_3348_top_two.md

@@ -0,0 +1,42 @@
+# Evidence Card: chr10.3348_top_two
+
+## Region
+- Locus: chr10:94334871-94334959
+- Cell context: K562
+
+## Top Target
+- Gene: IDE
+- Rank: 1
+- Score: 0.9961354232602443
+
+## Evidence
+- abc_score: 0.230474
+- available_t2s_signature: True
+- ccre_class: pELS
+- composition_context: K562 S2T composed with H1_hESC T2S (cross-context)
+- composition_method: weighted_sum_available_t2s_signatures
+- context_matched: False
+- distance_to_tss: -77398
+- is_nearest_gene: 0.0
+- n_targets_with_t2s_signature_used: 1
+- n_top_targets_considered: 5
+- s2t_model: logistic_distance_abc
+- s2t_split_family: chromosome_fold_3
+- signature_weight_sum: 0.569214
+
+## Predicted Response
+- score_type: weighted_mean_delta_expression
+- top_response_genes: [{"predicted_delta_expression": -2.73694, "response_gene": "IDE"}, {"predicted_delta_expression": -2.263214, "response_gene": "DNMT3B"}, {"predicted_delta_expression": -2.172841, "response_gene": "TUBB2B"}, {"predicted_delta_expression": -2.014252, "response_gene": "FLNA"}, {"predicted_delta_expression": -1.799169, "response_gene": "L1TD1"}]
+
+## Pathways
+- No pathway evidence supplied.
+
+## Uncertainty
+- not_calibrated_for_cross_context_composition
+
+## Caveats
+- K562 S2T and H1_hESC T2S are not matched biological contexts.
+- Composition uses only candidate targets with available T2S perturbation signatures.
+- Evidence is deterministic from computed features and does not assert an unsupported mechanism.
+- Prediction is model-derived and requires experimental validation.
+- Output is for research prioritization, not clinical interpretation.