POLYMER GENOMICSData sources·50 layers · versions · provenance
§ DATA SOURCES · 46 layers · versions · licenses · evidence classes
Data sources
Every layer the Polymer API serves, with its origin, version, license, and evidence class. Each response from the API carries a content hash and the same evidence-class tags — so downstream pipelines can audit, cache, and cite.
Evidence classesMMeasuredKCuratedDDerivedSStatisticalHHypothetical
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| Layer | Description | Version | Source | License | Count | Build | EV |
|---|---|---|---|---|---|---|---|
GENCODE v44 genesgencode_v44 · Reference | Comprehensive gene annotation — transcripts, exons, CDS, UTRs. | v44 · 2023-10 | GENCODE | CC BY 4.0 | 63,086 transcripts | hg38+hg37 | K |
RefSeq v224refseq_v224 · Reference | NCBI reference annotations · clinical-grade. | v224 · 2024-08 | NCBI | Public domain | 54,212 transcripts | hg38+hg37 | K |
GTEx v8 expressiongtex_v8 · Reference | Cross-tissue gene expression for 54 tissues. | v8 · 2019 | GTEx | dbGaP DUC | 54 tissues | hg38 | M |
gnomAD v4 constraintgnomad_v4 · Reference | Loss-of-function intolerance metrics — pLI, LOEUF, oe-syn. | v4 · 2024 | gnomAD | CC BY 4.0 | 730K exomes | hg38 | D |
Stacking ΔG₃₇stacking_dg37 · Biophysics | Nearest-neighbor stacking free energy at 37 °C, base-pair resolution. | v3.0 · 2026-02 | SantaLucia 2004 + curated | CC BY 4.0 | 3.20 Gb @ 1 bp | hg38+hg37 | D |
Melting temperaturemelting_tm · Biophysics | Predicted Tm at 50 mM Na⁺, 1 kb sliding window. | v3.0 · 2026-02 | SantaLucia | CC BY 4.0 | 3.20 Gb @ 1 kb | hg38+hg37 | D |
Intrinsic curvaturecurvature · Biophysics | Calladine-style curvature predictions, 30 bp window. | v2.4 · 2026-01 | Polymer Genomics | Polymer EULA | 3.20 Gb @ 1 bp | hg38 | D |
Major/minor groovegroove_width · Biophysics | Major and minor groove width + depth from DNA shape models. | v2.4 · 2026-01 | Polymer Genomics | Polymer EULA | 3.20 Gb @ 1 bp | hg38 | D |
A-form propensitya_form_prop · Biophysics | Sequence-encoded propensity to adopt A-form duplex. | v2.4 · 2026-01 | Polymer Genomics | Polymer EULA | 3.20 Gb @ 1 bp | hg38 | D |
Z-form propensityz_form_prop · Biophysics | Z-DNA propensity tied to alternating purine-pyrimidine. | v2.4 · 2026-01 | Polymer Genomics | Polymer EULA | 3.20 Gb @ 1 bp | hg38 | D |
Molar extinction (E₂₆₀)extinction_e260 · Biophysics | Per-base ε₂₆₀ for quantification calculations. | v1.0 · 2026-02 | Cantor & Warshaw | CC BY 4.0 | 3.20 Gb @ 1 bp | hg38+hg37 | D |
Biosynthetic costgene_costs_v1 · Biophysics | Per-amino-acid ATP-equivalent biosynthetic cost rolled up per gene. | v1.0 · 2025-11 | Polymer + Akashi | CC BY 4.0 | 19,427 genes | hg38 | D |
CpG sitescpg_sites · CpG / methylation | All CpG dinucleotide positions genome-wide. | 2024-08 | GRCh38 / GRCh37 | Public domain | 29,439,827 | hg38+hg37 | M |
CpG islandscpg_islands · CpG / methylation | Gardiner-Garden + Frommer CpG island calls. | 2024-08 | UCSC | Public domain | 235,847 | hg38+hg37 | K |
EPIC v2 probesprobe_epic_v2 · CpG / methylation | Illumina EPIC v2 array manifest with probe context. | v1.0 · 2023 | Illumina | Illumina | 937,690 | hg38 | M |
EPIC v1 probesprobe_epic_v1 · CpG / methylation | Illumina EPIC v1 array manifest. | v1.0 · 2016 | Illumina | Illumina | 865,918 | hg38+hg37 | M |
450K probesprobe_450k · CpG / methylation | Illumina HumanMethylation450 BeadChip. | v1.0 · 2011 | Illumina | Illumina | 485,577 | hg38+hg37 | M |
Methylation atlasmethylation_atlas · CpG / methylation | Reference WGBS methylation across 12 tissues. | v2.1 · 2024 | NIH Roadmap | CC BY 4.0 | 12 tissues | hg38 | M |
Epigenetic clocksclocks_v1 · CpG / methylation | 6 clocks: Horvath, Hannum, PhenoAge, GrimAge, Retro-Age, DunedinPACE. | v1.2 · 2026-01 | Curated · Polymer | CC BY-SA 4.0 | 6 clocks · 2,488 probes | hg38 | D |
Isochoresisochores · Structural | L1/L2/H1/H2/H3 isochore class per 100 kb bin. | v1.4 · 2025-09 | Polymer Genomics | CC BY-SA 4.0 | 34,000 bins | hg38 | D |
TAD domainstads_encode · Structural | TAD calls across 108 ENCODE cell types. | 2024 | ENCODE | CC BY 4.0 | 347,914 TADs | hg38 | M |
H3K4me3histone_h3k4me3 · Structural | Active promoter mark, ENCODE consolidated. | v3 · 2024 | ENCODE | CC BY 4.0 | 78 cell types | hg38 | M |
H3K27achistone_h3k27ac · Structural | Active enhancer mark. | v3 · 2024 | ENCODE | CC BY 4.0 | 92 cell types | hg38 | M |
H3K27me3histone_h3k27me3 · Structural | Polycomb repressive mark. | v3 · 2024 | ENCODE | CC BY 4.0 | 64 cell types | hg38 | M |
G-quadruplex predictionsg4_predicted · Structural | pqsfinder G4 motif predictions, per-strand. | v1.0 · 2024 | pqsfinder | CC BY 4.0 | 739,201 G4s | hg38 | D |
R-loop forming sequencesrloop_predicted · Structural | QmRLFS R-loop prediction. | v1.0 · 2024 | QmRLFS | CC BY 4.0 | 212,488 RLFS | hg38 | D |
RepeatMasker v4.1.9repeatmasker_v419 · Repeats | All annotated repeats (SINE/LINE/LTR/DNA/Satellite/Simple). | v4.1.9 · 2024 | Smit, Hubley & Green | Open | 5,632,191 | hg38+hg37 | K |
SINE / Alusine_alu · Repeats | Alu family subset with subfamily call (AluY/AluS/AluJ). | 2024 | RepeatMasker | Open | 1,094,000 Alus | hg38 | K |
LINE-1line_l1 · Repeats | L1 family with subfamily age (L1HS, L1PA2-7, L2). | 2024 | RepeatMasker | Open | 569,000 L1s | hg38 | K |
LTR / ERVltr_erv · Repeats | Endogenous retroviruses with subfamily annotation. | 2024 | RepeatMasker + curated | Open | 567,000 ERVs | hg38 | K |
HERV subfamily curationherv_subfamilies · Repeats | Manual subfamily refinement (HERV-K/H/W/E/L). | v1.2 · 2025-08 | Polymer Genomics | Polymer EULA | 6,464 ERVs | hg38 | K |
TE age (MYA)te_age · Repeats | Per-element evolutionary age from divergence. | v1.0 · 2025-10 | Polymer Genomics | Polymer EULA | 5.6M elements | hg38 | D |
TE awakening scorete_awakening · Repeats | Reactivation propensity score per TE family. | v1.0 · 2026-02 | Polymer Genomics | Polymer EULA | 17 families | hg38 | S |
ClinVarclinvar · Variants | Clinically reported variants with assertions. | 2024-09 | NCBI | Public domain | 2,847,212 | hg38+hg37 | K |
GWAS Cataloggwas_catalog · Variants | EBI GWAS Catalog SNP-trait associations. | 2024-08 | EBI | CC0 | 658,124 | hg38 | M |
dbSNP build 156dbsnp_b156 · Variants | Reference SNPs for variant annotation. | b156 · 2024 | NCBI | Public domain | ~1 B | hg38+hg37 | K |
IMGT/HLAimgt_hla · Clinical | Curated HLA allele sequences (32,867 alleles across 6 loci). | v3.55 · 2024 | IMGT/HLA | CC BY-ND 3.0 | 32,867 alleles | hg38 | K |
HLA non-coding divergencehla_ncds · Clinical | Per-allele NCDS score derived from non-coding biophysics. | v1.0 · 2026-03 | Polymer Genomics | Polymer EULA | 32,867 alleles | hg38 | D |
TCGAtcga · Clinical | Cancer methylation + RNA-seq, planned ingestion. | Pending | TCGA | dbGaP DUC | 11,000 samples | hg38 | M |
Contextual biophysicsbiophysics_compute · Compute | 8 property groups computable on-demand for any region ≤1 Mb. | v3.0 · 2026-02 | Polymer Genomics | Polymer EULA | 8 property groups | hg38+hg37 | D |
Sequence evaluatorevaluate_compute · Compute | Physics linter with 13 flag codes for ≤100 kb sequences. | v2.4 · 2026-01 | Polymer Genomics | Polymer EULA | 13 flag codes | — | D |
Aggregation serviceaggregation · Compute | Pre-binned layer counts, 1 kb–10 Mb resolution. | v1.0 · 2026-01 | Polymer Genomics | Polymer EULA | all layers | hg38+hg37 | D |
Clock predictionclocks_predict · Compute | Apply DNAm clock coefficients to beta matrices. | v1.0 · 2026-02 | Polymer Genomics | Polymer EULA | 6 clocks | hg38 | D |
Exp 17 · recombinationexp17_recomb · Compute | Per-region crossover-hotspot score (AUROC 0.827). | v1.0 · 2026-04 | Polymer Genomics | Polymer EULA | 1 score per region | hg38 | S |
Exp 03 · TE silencingexp03_te · Compute | Per-TE silencing score with biophysical feature attribution. | v1.0 · 2026-02 | Polymer Genomics | Polymer EULA | 5.6M scores | hg38 | S |
Exp 22 · CpG erosionexp22_age · Compute | TE-age estimate from CpG erosion chronometer. | v1.0 · 2026-05 | Polymer Genomics | Polymer EULA | 17 TE families | hg38 | S |
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