{ "benchmark_id": "finemap-coloc-scipy-v1", "validation_set_id": "VAL-SET-018-FINEMAP-COLOC-12COHORT", "timestamp_utc": "2026-11-02T23:59:00Z", "native_engine": "bio-suite 4-Stage Log-Space Wakefield ABF, 95% Credible Set Entropy & Giambartolomei 5-Hypothesis Colocalization Engine", "reference_tool": "SciPy v1.18.1 (scipy.special.logsumexp + coloc.abf)", "total_cohorts": 12, "dev_cohorts": 6, "reserve_cohorts": 6, "total_variants_evaluated": 240, "mae_lead_ln_abf": 0.0, "mae_lead_pip_gwas": 0.0, "mae_credible_entropy_bits": 0.0, "mae_coloc_pp_h3": 0.0, "mae_coloc_pp_h4": 0.0, "pearson_r_pip": 1.0, "pearson_r_pp_h4": 1.0, "credible_set_concordance_rate": 1.0, "regime_concordance_rate": 1.0, "native_runtime_ms": 0.5076, "scipy_runtime_ms": 8.5, "speedup_factor": 16.7455, "ascii_locus_profile": "========================================================================================================\n WAKEFIELD ABF FINE-MAPPING, 95% CREDIBLE SET & GIAMBARTOLOMEI COLOC (H0..H4) CALIBRATION (VAL-SET-018)\n========================================================================================================\n Cohort Split Locus (Cytoband) Lead SNP |CS95| PIP_1 PP.H3 PP.H4 Regime\n ------------------------------------------------------------------------------------------------------\n DEV-01 DEV SORT1 / CELSR2 / PSRC1 (1p13 rs12740374 1 1.0000 0.0000 1.0000 ColocalizedSingleCausalVariant\n DEV-02 DEV IL23R (R381Q Coding Protecti rs11209026 1 1.0000 0.0000 1.0000 ColocalizedSingleCausalVariant\n DEV-03 DEV APOE / TOMM40 (Cys112Arg eps rs429358 1 1.0000 0.0000 1.0000 ColocalizedSingleCausalVariant\n DEV-04 DEV CDKN2A / CDKN2B / ANRIL (4-S rs1333049 4 0.4917 0.0018 0.9982 ColocalizedCredibleLDBlock\n DEV-05 DEV MSMB (Promoter CREB Site -57 rs10993994 1 0.9631 0.0001 0.9999 ColocalizedSingleCausalVariant\n DEV-06 DEV Chr12q21 Intergenic Null Noi rs10762105 19 0.0850 0.0000 0.0000 UnderpoweredNullH0Control\n RES-01 RESERVE TYK2 (P1104A JH2 Pseudokinas rs34536443 1 1.0000 0.0000 1.0000 ColocalizedSingleCausalVariant\n RES-02 RESERVE PCSK9 (R46L Prodomain Loss-o rs11591147 1 1.0000 0.0000 1.0000 ColocalizedSingleCausalVariant\n RES-03 RESERVE SCN1A (3-SNP Intronic Promot rs6732655 2 0.6547 0.0009 0.9991 ColocalizedSingleCausalVariant\n RES-04 RESERVE SH2B1 / TUFM (3-SNP 16p11.2 rs7359397 3 0.6331 0.0010 0.9990 ColocalizedCredibleLDBlock\n RES-05 RESERVE ERAP2 (rs2248374 Splice-Dono rs2248374 1 1.0000 0.0000 1.0000 ColocalizedSingleCausalVariant\n RES-06 RESERVE MAPT vs. KANSL1 Distinct-Cau rs8070723 1 1.0000 1.0000 0.0000 DistinctLinkageH3Regime\n========================================================================================================\n", "cohorts": [ { "cohort_id": "DEV-01", "split": "Development", "locus_name": "SORT1 / CELSR2 / PSRC1", "cytoband": "1p13.3", "gwas_trait": "LDL-Cholesterol & Coronary Artery Disease (GLGC / CARDIoGRAM)", "molecular_qtl_trait": "Hepatocyte SORT1 cis-eQTL (GTEx v8 Liver)", "lead_rsid_gwas": "rs12740374", "lead_rsid_qtl": "rs12740374", "variant_count": 20, "is_negative_control": false, "native_lead_ln_abf_gwas": 55.3356, "native_lead_pip_gwas": 1.0, "native_lead_pip_qtl": 1.0, "native_credible_set_95_size": 1, "native_credible_set_95_coverage": 1.0, "native_credible_set_entropy_bits": 0.0, "native_pp_h0": 0.0, "native_pp_h1": 0.0, "native_pp_h2": 0.0, "native_pp_h3": 0.0, "native_pp_h4": 1.0, "native_pleiotropy_ratio": 1.0, "native_regime": "ColocalizedSingleCausalVariant", "scipy_lead_ln_abf_gwas": 55.3356, "scipy_lead_pip_gwas": 1.0, "scipy_lead_pip_qtl": 1.0, "scipy_credible_set_95_size": 1, "scipy_credible_set_95_coverage": 1.0, "scipy_credible_set_entropy_bits": 0.0, "scipy_pp_h0": 0.0, "scipy_pp_h1": 0.0, "scipy_pp_h2": 0.0, "scipy_pp_h3": 0.0, "scipy_pp_h4": 1.0, "scipy_pleiotropy_ratio": 1.0, "scipy_regime": "ColocalizedSingleCausalVariant", "abs_diff_ln_abf": 0.0, "abs_diff_pip_gwas": 0.0, "abs_diff_entropy_bits": 0.0, "abs_diff_pp_h3": 0.0, "abs_diff_pp_h4": 0.0, "credible_set_exact_match": true, "regime_concordant": true, "top_variants": [ { "rsid": "rs12740374", "position_bp": 109279570, "z_gwas": -10.8, "z_qtl": 11.4, "ln_abf_gwas": 55.3356, "ln_abf_qtl": 61.0965, "pip_gwas": 1.0, "pip_qtl": 1.0, "pip_coloc_h4": 1.0, "in_credible_set_95": true }, { "rsid": "rs646776", "position_bp": 109280820, "z_gwas": -9.1, "z_qtl": 9.5517, "ln_abf_gwas": 38.6683, "ln_abf_qtl": 42.3124, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs599839", "position_bp": 109282070, "z_gwas": -8.4, "z_qtl": 8.8, "ln_abf_gwas": 32.637, "ln_abf_qtl": 35.6017, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs10092720", "position_bp": 109298320, "z_gwas": 0.7563, "z_qtl": -0.4, "ln_abf_gwas": -1.1847, "ln_abf_qtl": -1.329, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs10092716", "position_bp": 109293320, "z_gwas": -0.7146, "z_qtl": 0.5526, "ln_abf_gwas": -1.2137, "ln_abf_qtl": -1.2607, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false } ] }, { "cohort_id": "DEV-02", "split": "Development", "locus_name": "IL23R (R381Q Coding Protection)", "cytoband": "1p31.3", "gwas_trait": "Crohn's Disease & Ulcerative Colitis (IIBDGC)", "molecular_qtl_trait": "Th17 Memory T-Cell IL23R pSTAT3 Signaling eQTL/sQTL", "lead_rsid_gwas": "rs11209026", "lead_rsid_qtl": "rs11209026", "variant_count": 20, "is_negative_control": false, "native_lead_ln_abf_gwas": 45.5891, "native_lead_pip_gwas": 1.0, "native_lead_pip_qtl": 1.0, "native_credible_set_95_size": 1, "native_credible_set_95_coverage": 1.0, "native_credible_set_entropy_bits": 0.0, "native_pp_h0": 0.0, "native_pp_h1": 0.0, "native_pp_h2": 0.0, "native_pp_h3": 0.0, "native_pp_h4": 1.0, "native_pleiotropy_ratio": 1.0, "native_regime": "ColocalizedSingleCausalVariant", "scipy_lead_ln_abf_gwas": 45.5891, "scipy_lead_pip_gwas": 1.0, "scipy_lead_pip_qtl": 1.0, "scipy_credible_set_95_size": 1, "scipy_credible_set_95_coverage": 1.0, "scipy_credible_set_entropy_bits": 0.0, "scipy_pp_h0": 0.0, "scipy_pp_h1": 0.0, "scipy_pp_h2": 0.0, "scipy_pp_h3": 0.0, "scipy_pp_h4": 1.0, "scipy_pleiotropy_ratio": 1.0, "scipy_regime": "ColocalizedSingleCausalVariant", "abs_diff_ln_abf": 0.0, "abs_diff_pip_gwas": 0.0, "abs_diff_entropy_bits": 0.0, "abs_diff_pp_h3": 0.0, "abs_diff_pp_h4": 0.0, "credible_set_exact_match": true, "regime_concordant": true, "top_variants": [ { "rsid": "rs11209026", "position_bp": 67249025, "z_gwas": -9.9489, "z_qtl": -10.2, "ln_abf_gwas": 45.5891, "ln_abf_qtl": 47.8522, "pip_gwas": 1.0, "pip_qtl": 1.0, "pip_coloc_h4": 1.0, "in_credible_set_95": true }, { "rsid": "rs10889677", "position_bp": 67250275, "z_gwas": -7.8, "z_qtl": -8.05, "ln_abf_gwas": 27.5529, "ln_abf_qtl": 29.1815, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs10672420", "position_bp": 67264025, "z_gwas": 0.7146, "z_qtl": -0.3763, "ln_abf_gwas": -1.2137, "ln_abf_qtl": -1.3376, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs10672416", "position_bp": 67259025, "z_gwas": -0.675, "z_qtl": 0.5211, "ln_abf_gwas": -1.2397, "ln_abf_qtl": -1.2766, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs10672407", "position_bp": 67247775, "z_gwas": -0.7196, "z_qtl": 0.5432, "ln_abf_gwas": -1.2496, "ln_abf_qtl": -1.1319, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false } ] }, { "cohort_id": "DEV-03", "split": "Development", "locus_name": "APOE / TOMM40 (Cys112Arg epsilon4)", "cytoband": "19q13.32", "gwas_trait": "Late-Onset Alzheimer's Disease (IGAP / EADB)", "molecular_qtl_trait": "Plasma ApoE Isoform Abundance cis-pQTL (UKB-PPP)", "lead_rsid_gwas": "rs429358", "lead_rsid_qtl": "rs429358", "variant_count": 20, "is_negative_control": false, "native_lead_ln_abf_gwas": 96.6932, "native_lead_pip_gwas": 1.0, "native_lead_pip_qtl": 1.0, "native_credible_set_95_size": 1, "native_credible_set_95_coverage": 1.0, "native_credible_set_entropy_bits": 0.0, "native_pp_h0": 0.0, "native_pp_h1": 0.0, "native_pp_h2": 0.0, "native_pp_h3": 0.0, "native_pp_h4": 1.0, "native_pleiotropy_ratio": 1.0, "native_regime": "ColocalizedSingleCausalVariant", "scipy_lead_ln_abf_gwas": 96.6932, "scipy_lead_pip_gwas": 1.0, "scipy_lead_pip_qtl": 1.0, "scipy_credible_set_95_size": 1, "scipy_credible_set_95_coverage": 1.0, "scipy_credible_set_entropy_bits": -0.0, "scipy_pp_h0": 0.0, "scipy_pp_h1": 0.0, "scipy_pp_h2": 0.0, "scipy_pp_h3": 0.0, "scipy_pp_h4": 1.0, "scipy_pleiotropy_ratio": 1.0, "scipy_regime": "ColocalizedSingleCausalVariant", "abs_diff_ln_abf": 0.0, "abs_diff_pip_gwas": 0.0, "abs_diff_entropy_bits": 0.0, "abs_diff_pp_h3": 0.0, "abs_diff_pp_h4": 0.0, "credible_set_exact_match": true, "regime_concordant": true, "top_variants": [ { "rsid": "rs429358", "position_bp": 44912434, "z_gwas": 14.2, "z_qtl": -12.6, "ln_abf_gwas": 96.6932, "ln_abf_qtl": 75.4291, "pip_gwas": 1.0, "pip_qtl": 1.0, "pip_coloc_h4": 1.0, "in_credible_set_95": true }, { "rsid": "rs4420638", "position_bp": 44914934, "z_gwas": 11.1, "z_qtl": -9.85, "ln_abf_gwas": 58.2835, "ln_abf_qtl": 45.3289, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs2075650", "position_bp": 44911184, "z_gwas": 10.5, "z_qtl": -9.4, "ln_abf_gwas": 51.9038, "ln_abf_qtl": 41.0627, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs10449020", "position_bp": 44932434, "z_gwas": 0.8, "z_qtl": -0.4211, "ln_abf_gwas": -1.1525, "ln_abf_qtl": -1.3209, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs10449016", "position_bp": 44927434, "z_gwas": -0.7542, "z_qtl": 0.5842, "ln_abf_gwas": -1.1862, "ln_abf_qtl": -1.2438, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false } ] }, { "cohort_id": "DEV-04", "split": "Development", "locus_name": "CDKN2A / CDKN2B / ANRIL (4-SNP Enhancer LD Block)", "cytoband": "9p21.3", "gwas_trait": "Coronary Artery Disease & Myocardial Infarction", "molecular_qtl_trait": "Coronary Smooth Muscle CDKN2B-AS1 cis-eQTL", "lead_rsid_gwas": "rs1333049", "lead_rsid_qtl": "rs1333049", "variant_count": 20, "is_negative_control": false, "native_lead_ln_abf_gwas": 26.7229, "native_lead_pip_gwas": 0.4917, "native_lead_pip_qtl": 0.5088, "native_credible_set_95_size": 4, "native_credible_set_95_coverage": 1.0, "native_credible_set_entropy_bits": 1.685, "native_pp_h0": 0.0, "native_pp_h1": 0.0, "native_pp_h2": 0.0, "native_pp_h3": 0.0018, "native_pp_h4": 0.9982, "native_pleiotropy_ratio": 0.9982, "native_regime": "ColocalizedCredibleLDBlock", "scipy_lead_ln_abf_gwas": 26.7229, "scipy_lead_pip_gwas": 0.4917, "scipy_lead_pip_qtl": 0.5088, "scipy_credible_set_95_size": 4, "scipy_credible_set_95_coverage": 1.0, "scipy_credible_set_entropy_bits": 1.685, "scipy_pp_h0": 0.0, "scipy_pp_h1": 0.0, "scipy_pp_h2": 0.0, "scipy_pp_h3": 0.0018, "scipy_pp_h4": 0.9982, "scipy_pleiotropy_ratio": 0.9982, "scipy_regime": "ColocalizedCredibleLDBlock", "abs_diff_ln_abf": 0.0, "abs_diff_pip_gwas": 0.0, "abs_diff_entropy_bits": 0.0, "abs_diff_pp_h3": 0.0, "abs_diff_pp_h4": 0.0, "credible_set_exact_match": true, "regime_concordant": true, "top_variants": [ { "rsid": "rs1333049", "position_bp": 22135503, "z_gwas": 7.65, "z_qtl": 7.8, "ln_abf_gwas": 26.7229, "ln_abf_qtl": 27.621, "pip_gwas": 0.4917, "pip_qtl": 0.5088, "pip_coloc_h4": 0.6964, "in_credible_set_95": true }, { "rsid": "rs4977574", "position_bp": 22136753, "z_gwas": 7.5786, "z_qtl": 7.72, "ln_abf_gwas": 26.1895, "ln_abf_qtl": 27.024, "pip_gwas": 0.2885, "pip_qtl": 0.2801, "pip_coloc_h4": 0.2249, "in_credible_set_95": true }, { "rsid": "rs10757278", "position_bp": 22138003, "z_gwas": 7.5, "z_qtl": 7.64, "ln_abf_gwas": 25.6085, "ln_abf_qtl": 26.4333, "pip_gwas": 0.1613, "pip_qtl": 0.1551, "pip_coloc_h4": 0.0697, "in_credible_set_95": true }, { "rsid": "rs2383207", "position_bp": 22139253, "z_gwas": 7.3607, "z_qtl": 7.5, "ln_abf_gwas": 24.5935, "ln_abf_qtl": 25.4142, "pip_gwas": 0.0585, "pip_qtl": 0.056, "pip_coloc_h4": 0.0091, "in_credible_set_95": true }, { "rsid": "rs10221220", "position_bp": 22149253, "z_gwas": 0.6729, "z_qtl": -0.3553, "ln_abf_gwas": -1.241, "ln_abf_qtl": -1.3449, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false } ] }, { "cohort_id": "DEV-05", "split": "Development", "locus_name": "MSMB (Promoter CREB Site -57C>T)", "cytoband": "10q11.23", "gwas_trait": "Prostate Adenocarcinoma Risk (PRACTICAL)", "molecular_qtl_trait": "Prostate Epithelium beta-Microseminoprotein cis-eQTL/pQTL", "lead_rsid_gwas": "rs10993994", "lead_rsid_qtl": "rs10993994", "variant_count": 20, "is_negative_control": false, "native_lead_ln_abf_gwas": 36.8982, "native_lead_pip_gwas": 0.9631, "native_lead_pip_qtl": 0.9857, "native_credible_set_95_size": 1, "native_credible_set_95_coverage": 0.9631, "native_credible_set_entropy_bits": 0.228, "native_pp_h0": 0.0, "native_pp_h1": 0.0, "native_pp_h2": 0.0, "native_pp_h3": 0.0001, "native_pp_h4": 0.9999, "native_pleiotropy_ratio": 0.9999, "native_regime": "ColocalizedSingleCausalVariant", "scipy_lead_ln_abf_gwas": 36.8982, "scipy_lead_pip_gwas": 0.9631, "scipy_lead_pip_qtl": 0.9857, "scipy_credible_set_95_size": 1, "scipy_credible_set_95_coverage": 0.9631, "scipy_credible_set_entropy_bits": 0.228, "scipy_pp_h0": 0.0, "scipy_pp_h1": 0.0, "scipy_pp_h2": 0.0, "scipy_pp_h3": 0.0001, "scipy_pp_h4": 0.9999, "scipy_pleiotropy_ratio": 0.9999, "scipy_regime": "ColocalizedSingleCausalVariant", "abs_diff_ln_abf": 0.0, "abs_diff_pip_gwas": 0.0, "abs_diff_entropy_bits": 0.0, "abs_diff_pp_h3": 0.0, "abs_diff_pp_h4": 0.0, "credible_set_exact_match": true, "regime_concordant": true, "top_variants": [ { "rsid": "rs10993994", "position_bp": 51556996, "z_gwas": 8.9, "z_qtl": -9.452, "ln_abf_gwas": 36.8982, "ln_abf_qtl": 41.6574, "pip_gwas": 0.9631, "pip_qtl": 0.9857, "pip_coloc_h4": 0.9994, "in_credible_set_95": true }, { "rsid": "rs10993995", "position_bp": 51558246, "z_gwas": 8.5192, "z_qtl": -8.98, "ln_abf_gwas": 33.637, "ln_abf_qtl": 37.425, "pip_gwas": 0.0369, "pip_qtl": 0.0143, "pip_coloc_h4": 0.0006, "in_credible_set_95": false }, { "rsid": "rs10515420", "position_bp": 51573246, "z_gwas": 0.7146, "z_qtl": -0.3763, "ln_abf_gwas": -1.2137, "ln_abf_qtl": -1.3376, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs10515416", "position_bp": 51568246, "z_gwas": -0.675, "z_qtl": 0.5211, "ln_abf_gwas": -1.2397, "ln_abf_qtl": -1.2766, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false }, { "rsid": "rs10515411", "position_bp": 51561996, "z_gwas": 0.7152, "z_qtl": -0.6409, "ln_abf_gwas": -1.2525, "ln_abf_qtl": -1.0786, "pip_gwas": 0.0, "pip_qtl": 0.0, "pip_coloc_h4": 0.0, "in_credible_set_95": false } ] }, { "cohort_id": "DEV-06", "split": "Development", "locus_name": "Chr12q21 Intergenic Null Noise Control (H0 Negative Control)", "cytoband": "12q21.2", "gwas_trait": "Simulated Null Case-Control Phenotype (No Association)", "molecular_qtl_trait": "Subcutaneous Adipose Background Transcript Noise", "lead_rsid_gwas": "rs10762105", "lead_rsid_qtl": "rs10762104", "variant_count": 20, "is_negative_control": true, "native_lead_ln_abf_gwas": -0.8537, "native_lead_pip_gwas": 0.085, "native_lead_pip_qtl": 0.0723, "native_credible_set_95_size": 19, "native_credible_set_95_coverage": 0.959, "native_credible_set_entropy_bits": 4.3005, "native_pp_h0": 0.9989, "native_pp_h1": 0.0005, "native_pp_h2": 0.0006, "native_pp_h3": 0.0, "native_pp_h4": 0.0, "native_pleiotropy_ratio": 0.9813, "native_regime": "UnderpoweredNullH0Control", "scipy_lead_ln_abf_gwas": -0.8537, "scipy_lead_pip_gwas": 0.085, "scipy_lead_pip_qtl": 0.0723, "scipy_credible_set_95_size": 19, "scipy_credible_set_95_coverage": 0.959, "scipy_credible_set_entropy_bits": 4.3005, "scipy_pp_h0": 0.9989, "scipy_pp_h1": 0.0005, "scipy_pp_h2": 0.0006, "scipy_pp_h3": 0.0, "scipy_pp_h4": 0.0, "scipy_pleiotropy_ratio": 0.9813, "scipy_regime": "UnderpoweredNullH0Control", "abs_diff_ln_abf": 0.0, "abs_diff_pip_gwas": 0.0, "abs_diff_entropy_bits": 0.0, "abs_diff_pp_h3": 0.0, "abs_diff_pp_h4": 0.0, "credible_set_exact_match": true, "regime_concordant": true, "top_variants": [ { "rsid": "rs10762105", "position_bp": 76215000, "z_gwas": 1.18, "z_qtl": 0.42, "ln_abf_gwas": -0.8537, "ln_abf_qtl": -1.2738, "pip_gwas": 0.085, "pip_qtl": 0.0479, "pip_coloc_h4": 0.0815, "in_credible_set_95": true }, { "rsid": "rs10762120", "position_bp": 76233750, "z_gwas": 0.5896, "z_qtl": -0.3105, "ln_abf_gwas": -1.2908, "ln_abf_qtl": -1.3588, "pip_gwas": 0.0549, "pip_qtl": 0.044, "pip_coloc_h4": 0.0484, "in_credible_set_95": true }, { "rsid": "rs10762116", "position_bp": 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