{ "dataset_name": "Quantum Krump Somatic Motor-Unit & Peripheral-Clock Empirical Panel (AlphaGenome 2)", "generated_at_utc": "2026-11-11T22:06:51.763039+00:00", "alphagenome_sdk_version": "2.0.0", "reference_assembly": "GRCh38 / GENCODE v46 MANE Select", "research_use_only_disclosure": "Strictly non-clinical molecular and functional regulatory predictions. Condition embeddings reflect observational steady-state single-cell profiles (Gayoso et al., 2026, p. 14; Kedlian et al., 2024) rather than dynamic acute-exercise transitions.", "ag2_cell_state_specificity": { "ACTN3": { "gene": "ACTN3", "gene_id": "ENSG00000248746.6", "transcript_id": "ENST00000513398.2", "chrom": "chr11", "start": 66546902, "end": 66563334, "strand": "+", "tss": 66546902, "role": "Fast-twitch Z-disc alpha-actinin-3", "atlas_gene_url": "https://deepmind.google.com/science/alphagenome/atlas?q=ACTN3&m=entity", "conditions": { "gastrocnemius_fast_myocyte": { "condition_curie": "UBERON:0001388_CL:0000190", "sc_gene_expression_10x3_nuclear": 59.4945, "promoter_2kb_mean_cpg_methylation": 0.0091 }, "gastrocnemius_slow_myocyte": { "condition_curie": "UBERON:0001388_CL:0000189", "sc_gene_expression_10x3_nuclear": 47.0525, "promoter_2kb_mean_cpg_methylation": 0.0126 }, "motor_neuron": { "condition_curie": "CL:0000100", "sc_gene_expression_10x3_nuclear": 0.5885, "promoter_2kb_mean_cpg_methylation": 0.0206 } }, "fast_vs_motor_neuron_fold": 101.1, "fast_vs_slow_myocyte_fold": 1.2644 }, "MYH1": { "gene": "MYH1", "gene_id": "ENSG00000109061.10", "transcript_id": "ENST00000226207.6", "chrom": "chr17", "start": 10492306, "end": 10518542, "strand": "-", "tss": 10518542, "role": "Fast-twitch Type IIX myosin heavy chain 1", "atlas_gene_url": "https://deepmind.google.com/science/alphagenome/atlas?q=MYH1&m=entity", "conditions": { "gastrocnemius_fast_myocyte": { "condition_curie": "UBERON:0001388_CL:0000190", "sc_gene_expression_10x3_nuclear": 274.3315, "promoter_2kb_mean_cpg_methylation": 0.0101, "MYHAS_antisense_switch_10x3_nuclear": 60.8259 }, "gastrocnemius_slow_myocyte": { "condition_curie": "UBERON:0001388_CL:0000189", "sc_gene_expression_10x3_nuclear": 299.2764, "promoter_2kb_mean_cpg_methylation": 0.0125, "MYHAS_antisense_switch_10x3_nuclear": 10.2445 }, "motor_neuron": { "condition_curie": "CL:0000100", "sc_gene_expression_10x3_nuclear": 0.1189, "promoter_2kb_mean_cpg_methylation": 0.0108, "MYHAS_antisense_switch_10x3_nuclear": 0.7818 } }, "fast_vs_motor_neuron_fold": 2307.25, "fast_vs_slow_myocyte_fold": 0.9166 }, "ACTA1": { "gene": "ACTA1", "gene_id": "ENSG00000143632.15", "transcript_id": "ENST00000366684.7", "chrom": "chr1", "start": 229431244, "end": 229434094, "strand": "-", "tss": 229434094, "role": "Skeletal muscle alpha-actin", "atlas_gene_url": "https://deepmind.google.com/science/alphagenome/atlas?q=ACTA1&m=entity", "conditions": { "gastrocnemius_fast_myocyte": { "condition_curie": "UBERON:0001388_CL:0000190", "sc_gene_expression_10x3_nuclear": 497.3474, "promoter_2kb_mean_cpg_methylation": 0.0098 }, "gastrocnemius_slow_myocyte": { "condition_curie": "UBERON:0001388_CL:0000189", "sc_gene_expression_10x3_nuclear": 1254.0004, "promoter_2kb_mean_cpg_methylation": 0.0141 }, "motor_neuron": { "condition_curie": "CL:0000100", "sc_gene_expression_10x3_nuclear": 1.0422, "promoter_2kb_mean_cpg_methylation": 0.0223 } }, "fast_vs_motor_neuron_fold": 477.21, "fast_vs_slow_myocyte_fold": 0.3966 }, "CHRNA1": { "gene": "CHRNA1", "gene_id": "ENSG00000138435.16", "transcript_id": "ENST00000348749.9", "chrom": "chr2", "start": 174747591, "end": 174764472, "strand": "-", "tss": 174764472, "role": "Postsynaptic NMJ nicotinic acetylcholine receptor alpha-1", "atlas_gene_url": "https://deepmind.google.com/science/alphagenome/atlas?q=CHRNA1&m=entity", "conditions": { "gastrocnemius_fast_myocyte": { "condition_curie": "UBERON:0001388_CL:0000190", "sc_gene_expression_10x3_nuclear": 22.4852, "promoter_2kb_mean_cpg_methylation": 0.0088 }, "gastrocnemius_slow_myocyte": { "condition_curie": "UBERON:0001388_CL:0000189", "sc_gene_expression_10x3_nuclear": 55.972, "promoter_2kb_mean_cpg_methylation": 0.0103 }, "motor_neuron": { "condition_curie": "CL:0000100", "sc_gene_expression_10x3_nuclear": 0.367, "promoter_2kb_mean_cpg_methylation": 0.0142 } }, "fast_vs_motor_neuron_fold": 61.27, "fast_vs_slow_myocyte_fold": 0.4017 }, "PER2": { "gene": "PER2", "gene_id": "ENSG00000132326.13", "transcript_id": "ENST00000254657.8", "chrom": "chr2", "start": 238244043, "end": 238288610, "strand": "-", "tss": 238288610, "role": "Peripheral circadian clock oscillator (ubiquitous control)", "atlas_gene_url": "https://deepmind.google.com/science/alphagenome/atlas?q=PER2&m=entity", "conditions": { "gastrocnemius_fast_myocyte": { "condition_curie": "UBERON:0001388_CL:0000190", "sc_gene_expression_10x3_nuclear": 5.8788, "promoter_2kb_mean_cpg_methylation": 0.0088 }, "gastrocnemius_slow_myocyte": { "condition_curie": "UBERON:0001388_CL:0000189", "sc_gene_expression_10x3_nuclear": 5.7347, "promoter_2kb_mean_cpg_methylation": 0.011 }, "motor_neuron": { "condition_curie": "CL:0000100", "sc_gene_expression_10x3_nuclear": 8.3164, "promoter_2kb_mean_cpg_methylation": 0.0191 } }, "fast_vs_motor_neuron_fold": 0.71, "fast_vs_slow_myocyte_fold": 1.0251 } }, "somatic_20_variant_panel": [ { "gene": "ACTN3", "role": "Fast-twitch Z-disc alpha-actinin-3 (R577X stop-gain)", "variant": "chr11:66560624:C>T", "avi_raw": 1.549325, "avi_tail_quantile": 0.00108325, "avi_phred": 29.6527, "top_modality": "PROTEIN_TERMINATION", "top_feature_importance": 1.411512, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr11:66560624:C%3ET&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.99891675 }, { "gene": "ACTN3", "role": "Fast-twitch Z-disc alpha-actinin-3 (TSS promoter window)", "variant": "chr11:66546927:G>C", "avi_raw": 0.100088, "avi_tail_quantile": 0.15246511, "avi_phred": 8.1683, "top_modality": "MAX_ABS_PROCAP", "top_feature_importance": 0.032937, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr11:66546927:G%3EC&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.84753489 }, { "gene": "ACTN3", "role": "Fast-twitch Z-disc alpha-actinin-3 (TSS promoter window)", "variant": "chr11:66546925:G>T", "avi_raw": 0.284153, "avi_tail_quantile": 0.03977144, "avi_phred": 14.0043, "top_modality": "PHASTCONS_470_WAY", "top_feature_importance": 0.154648, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr11:66546925:G%3ET&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.96022856 }, { "gene": "ACTN3", "role": "Fast-twitch Z-disc alpha-actinin-3 (TSS promoter window)", "variant": "chr11:66546905:G>A", "avi_raw": 0.48498, "avi_tail_quantile": 0.0139845, "avi_phred": 18.5435, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.19193, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr11:66546905:G%3EA&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.9860155 }, { "gene": "MYH1", "role": "Fast-twitch Type IIX myosin heavy chain 1 (TSS promoter window)", "variant": "chr17:10518554:A>T", "avi_raw": 0.342706, "avi_tail_quantile": 0.02783662, "avi_phred": 15.5538, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.174605, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr17:10518554:A%3ET&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.97216338 }, { "gene": "MYH1", "role": "Fast-twitch Type IIX myosin heavy chain 1 (TSS promoter window)", "variant": "chr17:10518541:A>T", "avi_raw": 0.456912, "avi_tail_quantile": 0.01568943, "avi_phred": 18.0439, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.283606, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr17:10518541:A%3ET&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.98431057 }, { "gene": "MYH1", "role": "Fast-twitch Type IIX myosin heavy chain 1 (TSS promoter window)", "variant": "chr17:10518539:A>G", "avi_raw": 0.600266, "avi_tail_quantile": 0.00873202, "avi_phred": 20.5889, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.380558, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr17:10518539:A%3EG&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.99126798 }, { "gene": "MYH1", "role": "Fast-twitch Type IIX myosin heavy chain 1 (TSS promoter window)", "variant": "chr17:10518520:C>G", "avi_raw": 1.147912, "avi_tail_quantile": 0.00303644, "avi_phred": 25.1764, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.540201, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr17:10518520:C%3EG&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.99696356 }, { "gene": "ACTA1", "role": "Skeletal muscle alpha-actin (TSS promoter window)", "variant": "chr1:229434112:C>A", "avi_raw": 0.102763, "avi_tail_quantile": 0.14919651, "avi_phred": 8.2624, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.049651, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr1:229434112:C%3EA&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.85080349 }, { "gene": "ACTA1", "role": "Skeletal muscle alpha-actin (TSS promoter window)", "variant": "chr1:229434078:G>T", "avi_raw": 0.240337, "avi_tail_quantile": 0.05338699, "avi_phred": 12.7256, "top_modality": "PHASTCONS_470_WAY", "top_feature_importance": 0.138353, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr1:229434078:G%3ET&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.94661301 }, { "gene": "ACTA1", "role": "Skeletal muscle alpha-actin (TSS promoter window)", "variant": "chr1:229434081:C>A", "avi_raw": 0.385344, "avi_tail_quantile": 0.02212656, "avi_phred": 16.5509, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.171732, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr1:229434081:C%3EA&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.97787344 }, { "gene": "ACTA1", "role": "Skeletal muscle alpha-actin (TSS promoter window)", "variant": "chr1:229434093:G>T", "avi_raw": 0.621342, "avi_tail_quantile": 0.00822228, "avi_phred": 20.8501, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.411347, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr1:229434093:G%3ET&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.99177772 }, { "gene": "CHRNA1", "role": "Postsynaptic NMJ nicotinic acetylcholine receptor alpha-1 (TSS promoter window)", "variant": "chr2:174764478:A>C", "avi_raw": 0.070348, "avi_tail_quantile": 0.1985395, "avi_phred": 7.0215, "top_modality": "MERGED_SPLICING", "top_feature_importance": 0.026505, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr2:174764478:A%3EC&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.8014605 }, { "gene": "CHRNA1", "role": "Postsynaptic NMJ nicotinic acetylcholine receptor alpha-1 (TSS promoter window)", "variant": "chr2:174764464:T>G", "avi_raw": 0.182579, "avi_tail_quantile": 0.08075279, "avi_phred": 10.9284, "top_modality": "MERGED_SPLICING", "top_feature_importance": 0.065153, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr2:174764464:T%3EG&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.91924721 }, { "gene": "CHRNA1", "role": "Postsynaptic NMJ nicotinic acetylcholine receptor alpha-1 (TSS promoter window)", "variant": "chr2:174764461:G>C", "avi_raw": 0.333002, "avi_tail_quantile": 0.02948242, "avi_phred": 15.3044, "top_modality": "PHASTCONS_470_WAY", "top_feature_importance": 0.149607, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr2:174764461:G%3EC&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.97051758 }, { "gene": "CHRNA1", "role": "Postsynaptic NMJ nicotinic acetylcholine receptor alpha-1 (TSS promoter window)", "variant": "chr2:174764485:G>A", "avi_raw": 0.655514, "avi_tail_quantile": 0.00731379, "avi_phred": 21.3586, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.279562, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr2:174764485:G%3EA&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.99268621 }, { "gene": "PER2", "role": "Peripheral circadian clock oscillator (ubiquitous control) (TSS promoter window)", "variant": "chr2:238288617:G>A", "avi_raw": 0.006429, "avi_tail_quantile": 0.45893562, "avi_phred": 3.3825, "top_modality": "MERGED_SPLICING", "top_feature_importance": 0.024197, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr2:238288617:G%3EA&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.54106438 }, { "gene": "PER2", "role": "Peripheral circadian clock oscillator (ubiquitous control) (TSS promoter window)", "variant": "chr2:238288602:G>C", "avi_raw": 0.081447, "avi_tail_quantile": 0.17886722, "avi_phred": 7.4747, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.058568, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr2:238288602:G%3EC&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.82113278 }, { "gene": "PER2", "role": "Peripheral circadian clock oscillator (ubiquitous control) (TSS promoter window)", "variant": "chr2:238288625:G>C", "avi_raw": 0.171874, "avi_tail_quantile": 0.08742094, "avi_phred": 10.5838, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.145335, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr2:238288625:G%3EC&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.91257906 }, { "gene": "PER2", "role": "Peripheral circadian clock oscillator (ubiquitous control) (TSS promoter window)", "variant": "chr2:238288608:A>C", "avi_raw": 0.523194, "avi_tail_quantile": 0.0116449, "avi_phred": 19.3386, "top_modality": "CACTUS_241_WAY", "top_feature_importance": 0.260802, "atlas_url": "https://deepmind.google.com/science/alphagenome/atlas?q=chr2:238288608:A%3EC&m=variant&lItems=avi,section:RNA_SEQ,section:DNASE,section:CHIP_TF", "avi_cdf_quantile": 0.9883551 } ], "panel_summary": { "n_variants": 20, "avi_raw_mean": 0.417026, "avi_raw_std": 0.370412, "avi_raw_min": 0.006429, "avi_raw_max": 1.549325, "avi_phred_mean": 15.1757, "avi_phred_max": 29.6527, "standardized_z_scores": [ 3.056865, -0.855636, -0.358716, 0.183456, -0.200641, 0.107681, 0.494693, 1.973171, -0.848414, -0.477006, -0.085531, 0.551592, -0.935925, -0.632935, -0.226839, 0.643846, -1.108487, -0.905961, -0.661835, 0.286622 ] } }