POLYMER GENOMICS
ViewerAtlasClaimsNewsroomDev / API

DATA SOURCES

Polymer Genomics aggregates data from the following public databases and published literature. Each source retains its original license. Please cite the original data providers when using their data in publications.

Note on licenses: Human Protein Atlas data is licensed under CC BY-SA 3.0 (ShareAlike). Any derivative works incorporating HPA data must be shared under the same license. GTEx data served here consists of summary statistics (median TPM by tissue) and does not include individual-level data, which requires dbGaP authorization.

Copyleft obligations: gnomAD data is licensed under ODC-ODbL 1.0, which requires derivative databases to remain open. CpG islands, RepeatMasker annotations, and conservation scores are independently computed by Polymer Genomics using open-source tools and public-domain reference data — no non-commercial restrictions apply to these layers.

Epigenetic clock IP: Some epigenetic clocks are protected by patents (e.g., GrimAge: US Patent 10,706,957). DunedinPACE may have separate intellectual property protections. Clock probe annotations served here are for informational and reference purposes only. Computation of epigenetic age using these coefficients may require separate licensing from the respective intellectual property holders.

Sequence & Assembly

SourceVersionRowsLicenseCitation
GRCh38 / hg38GCA_000001405.15—Public DomainGenome Reference Consortium
GRCh37 / hg37GCA_000001405.1—Public DomainGenome Reference Consortium
UCSC Genome Browser2024—Free for non-commercial useKent et al., Genome Res 2002

Gene Annotation

SourceVersionRowsLicenseCitation
GENCODEv44—CC0 1.0Frankish et al., Nucleic Acids Res 2021
RefSeqGCF_000001405.40—Public DomainO'Leary et al., Nucleic Acids Res 2016

Methylation & CpG

SourceVersionRowsLicenseCitation
Illumina EPIC v2 Manifestv2.0—Coordinates only (factual data)Illumina Inc. Probe IDs and genomic coordinates via sesameData.
Illumina EPIC v1 Manifestv1.0—Coordinates only (factual data)Pidsley et al., Genome Biol 2016. Probe IDs and genomic coordinates via sesameData.
Illumina 450K Manifestv1.2—Coordinates only (factual data)Bibikova et al., Genomics 2011. Probe IDs and genomic coordinates via sesameData.
CpG Islandshg38—MIT (computed)Gardiner-Garden & Frommer 1987. Computed from reference FASTA.

Expression

SourceVersionRowsLicenseCitation
GTExv10—dbGaP (summary statistics: open access)GTEx Consortium, Science 2020
Human Protein Atlasv23—CC BY-SA 3.0Uhlén et al., Science 2015
PaxDbv5.0—CC BY 4.0Wang et al., Mol Cell Proteomics 2015

Constraint & Variation

SourceVersionRowsLicenseCitation
gnomAD Constraintv4.1—ODC-ODbL 1.0Chen et al., Nature 2024
gnomAD Structural Variantsv4.1—ODC-ODbL 1.0Collins et al., Nature 2020
ClinVar2024-09—Public DomainLandrum et al., Nucleic Acids Res 2020

Pathways & Gene Sets

SourceVersionRowsLicenseCitation
Reactomev88—CC BY 4.0Gillespie et al., Nucleic Acids Res 2022
MSigDB Hallmarkv2024.1—CC BY 4.0Liberzon et al., Cell Syst 2015

Chromatin & Epigenomics

SourceVersionRowsLicenseCitation
ENCODE cCREsv4—CC BY 4.0ENCODE Consortium, Nature 2012
ENCODE Histone Peaksv3—CC BY 4.0ENCODE Consortium, Nature 2012
ENCODE TF Binding Sitesv3—CC BY 4.0ENCODE Consortium, Nature 2020
ENCODE Accessibility Signalv3—CC BY 4.0ENCODE Consortium, Nature 2020
ChromHMM 15-state Model2012—Public Domain (NIH)Ernst & Kellis, Nat Methods 2012
Roadmap Epigenomics2015—Public Domain (NIH)Roadmap Consortium, Nature 2015

3D Genome

SourceVersionRowsLicenseCitation
ENCODE TAD DomainsArrowhead—CC BY 4.0Rao et al., Cell 2014
Hi-C A/B Compartmentsv1—CC BY 4.0Lieberman-Aiden et al., Science 2009
Insulation Scorev1—CC BY 4.0Crane et al., Nature 2015
LADsMeuleman 2013—Published literatureMeuleman et al., Genome Res 2013
NADsv1—Published literatureNemeth et al., PLoS Genet 2010

Biophysics & Thermodynamics

SourceVersionRowsLicenseCitation
SantaLucia NN Parameters1998/2004—Published literatureSantaLucia, Proc Natl Acad Sci 1998; SantaLucia & Hicks, Annu Rev Biophys 2004
Sugimoto RNA/DNA Parameters1995—Published literatureSugimoto et al., Biochemistry 1995
Xia RNA Parameters1998—Published literatureXia et al., Biochemistry 1998

Epigenetic Clocks

SourceVersionRowsLicenseCitation
Horvath Clock2013—Published literatureHorvath, Genome Biol 2013
Hannum Clock2013—Published literatureHannum et al., Mol Cell 2013
PhenoAge2018—Published literatureLevine et al., Aging 2018
GrimAge2019—Published literatureLu et al., Aging 2019
DunedinPACE2022—Published literatureBelsky et al., eLife 2022

Mutations

SourceVersionRowsLicenseCitation
SBS Mutation Thermodynamicsv1.0—MIT (computed)SantaLucia, PNAS 1998. 96-channel trinucleotide stacking energy perturbations.

Conservation & Evolution

SourceVersionRowsLicenseCitation
Zoonomia phyloP 447-way2023—Freely usable for any purposeZoonomia Consortium, Science 2023; Cactus 447-way vertebrate alignment
phastCons 470-way2023—Freely usable for any purposeSiepel et al., Genome Res 2005; 470-way Cactus alignment
Ensembl Comparav112—Apache 2.0Herrero et al., Database 2016
Ultraconserved ElementsBejerano 2004—Published literatureBejerano et al., Science 2004
Human Accelerated Regionsv1—Published literaturePollard et al., Nature 2006
Archaic IntrogressionVernot 2016—Published literatureVernot et al., Science 2016
Selection Sweepsv1—Published literatureSabeti et al., Nature 2007

Repeat Elements & Transposons

SourceVersionRowsLicenseCitation
RepeatMaskerv4.1.5—Open Source + Dfam CC0 (self-computed)Smit, Hubley & Green, RepeatMasker Open-4.0 + Dfam 3.x
Telescope HERV Lociv2—MITBendall et al., PLoS Comput Biol 2019
TE Exaptation Catalogv1—CC BY 4.0Chuong et al., Nat Rev Genet 2017

GWAS

SourceVersionRowsLicenseCitation
EBI GWAS Catalogv1.0.4—CC0 1.0Buniello et al., Nucleic Acids Res 2019

Cell-Type Methylation

SourceVersionRowsLicenseCitation
FlowSorted.Blood.EPIC2018—Artistic License 2.0Salas et al., Genome Biol 2018
WGBS HematopoieticBLUEPRINT—CC BY 4.0Stunnenberg et al., Cell 2016
Archaic Methylationv1—Published literatureGokhman et al., Science 2014

Protein Properties & Turnover

SourceVersionRowsLicenseCitation
UniProt2024_05—CC BY 4.0UniProt Consortium, Nucleic Acids Res 2023
Protein Half-Lives2018—Published literatureMathieson et al., Nat Commun 2018

QTLs

SourceVersionRowsLicenseCitation
GTEx eQTLsv8—dbGaP (summary statistics: open access)GTEx Consortium, Science 2020
GoDMC meQTLsv1—Published literatureMin et al., Nat Genet 2021

Regulatory Elements

SourceVersionRowsLicenseCitation
ABC Enhancer-Gene Linksv1—CC BY 4.0Fulco et al., Nat Genet 2019
dbSUPER Super-Enhancersv1—Published literatureKhan & Zhang, Nucleic Acids Res 2016
DNA Methylation Valleysv1—Published literatureJeong et al., Genome Res 2014

Recombination

SourceVersionRowsLicenseCitation
Crossover HotspotsPalsson 2025—Published literaturePalsson et al., Science 2025
DMC1 Meiotic HotspotsPratto 2014—Published literaturePratto et al., Science 2014

Structural DNA & Fragility

SourceVersionRowsLicenseCitation
Non-B DNA Structuresv1—MITPolymer Genomics — G4, Z-DNA, cruciform, triplex, R-loop predictions
Fragility Composite Scorev1—MITPolymer Genomics — integrated from non-B, stacking, curvature
Recurrent Breakpointsv1—Published literatureHumCFS (Mrasek 2010) + Mitelman Database. Fragile sites and translocation breakpoints.

HLA

SourceVersionRowsLicenseCitation
IPD-IMGT/HLA Database3.55—CC BY 4.0Robinson et al., Nucleic Acids Res 2020

Mutation Density

SourceVersionRowsLicenseCitation
PCAWG Mutation Ratesv1—CC BY 4.0ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Nature 2020

Computed Tracks

SourceVersionRowsLicenseCitation
Polymer Evolution Layer 0v1.0—MITPolymer Genomics — computed from SantaLucia/published parameters
Viewer·Atlas·Claims·Newsroom·Dev / API·Terms·Privacy·Data Sources
RESEARCH USE ONLY·© 2026 Polymer Genomics