Trait: LDL cholesterol

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004195
Description Cholesterol which is contained in or bound to low density lipoproteins (LDL), including CHOLESTEROL ESTERS and free cholesterol.
Trait category
Other trait
Synonyms 5 synonyms
  • High-density lipoprotein cholesterol
  • High-density lipoproteins
  • LDL lipoproteins
  • cholesterol, LDL
  • lipoproteins, LDL

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS019798
(TPMI_HDL-C_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 HDL cholesterol LDL cholesterol 32,998
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019798/ScoringFiles/PGS019798.txt.gz
PGS019801
(TPMI_LDL-C_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 LDL cholesterol LDL cholesterol 3,616
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019801/ScoringFiles/PGS019801.txt.gz
PGS019822
(TPMI_HDL-C_LDPred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 HDL cholesterol LDL cholesterol 939,781
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019822/ScoringFiles/PGS019822.txt.gz
PGS019825
(TPMI_LDL-C_LDPred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 LDL cholesterol LDL cholesterol 939,820
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019825/ScoringFiles/PGS019825.txt.gz
PGS019846
(TPMI_HDL-C_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 HDL cholesterol LDL cholesterol 983,740
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019846/ScoringFiles/PGS019846.txt.gz
PGS019849
(TPMI_LDL-C_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 LDL cholesterol LDL cholesterol 983,774
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019849/ScoringFiles/PGS019849.txt.gz
PGS019870
(TPMI_HDL-C_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 HDL cholesterol LDL cholesterol 992,245
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019870/ScoringFiles/PGS019870.txt.gz
PGS019873
(TPMI_LDL-C_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 LDL cholesterol LDL cholesterol 996,216
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019873/ScoringFiles/PGS019873.txt.gz
PGS019894
(TPMI_HDL-C_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 HDL cholesterol LDL cholesterol 368,324
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019894/ScoringFiles/PGS019894.txt.gz
PGS019897
(TPMI_LDL-C_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 LDL cholesterol LDL cholesterol 299,576
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019897/ScoringFiles/PGS019897.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM037980 PGS019798
(TPMI_HDL-C_Lassosum2)
 PSS013735|
East Asian Ancestry|
8,059 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: High-density lipoprotein cholesterol — AUROC: 0.9054 R²: 0.13903 sex, age, array, PCs 1-10 —
PPM037983 PGS019801
(TPMI_LDL-C_Lassosum2)
 PSS013756|
East Asian Ancestry|
10,071 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Low-density lipoprotein cholesterol — AUROC: 0.7505 R²: 0.06971 sex, age, array, PCs 1-10 —
PPM038004 PGS019822
(TPMI_HDL-C_LDPred2)
 PSS013734|
East Asian Ancestry|
8,059 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: High-density lipoprotein cholesterol — AUROC: 0.62244 R²: 0.13809 sex, age, array, PCs 1-10 —
PPM038007 PGS019825
(TPMI_LDL-C_LDPred2)
 PSS013755|
East Asian Ancestry|
10,071 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Low-density lipoprotein cholesterol — AUROC: 0.68579 R²: 0.06938 sex, age, array, PCs 1-10 —
PPM038028 PGS019846
(TPMI_HDL-C_PRS-CS)
 PSS013737|
East Asian Ancestry|
8,059 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: High-density lipoprotein cholesterol — — R²: 0.14666 sex, age, array, PCs 1-10 —
PPM038031 PGS019849
(TPMI_LDL-C_PRS-CS)
 PSS013758|
East Asian Ancestry|
10,071 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Low-density lipoprotein cholesterol — — R²: 0.07192 sex, age, array, PCs 1-10 —
PPM038052 PGS019870
(TPMI_HDL-C_SBayesR)
 PSS013738|
East Asian Ancestry|
8,059 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: High-density lipoprotein cholesterol — AUROC: 0.69172 R²: 0.10529 sex, age, array, PCs 1-10 —
PPM038055 PGS019873
(TPMI_LDL-C_SBayesR)
 PSS013759|
East Asian Ancestry|
10,071 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Low-density lipoprotein cholesterol — AUROC: 0.7865 R²: 0.0492 sex, age, array, PCs 1-10 —
PPM038076 PGS019894
(TPMI_HDL-C_MegaPRS)
 PSS013736|
East Asian Ancestry|
8,059 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: High-density lipoprotein cholesterol — AUROC: 0.74988 R²: 0.09762 sex, age, array, PCs 1-10 —
PPM038079 PGS019897
(TPMI_LDL-C_MegaPRS)
 PSS013757|
East Asian Ancestry|
10,071 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Low-density lipoprotein cholesterol — AUROC: 0.81711 R²: 0.03612 sex, age, array, PCs 1-10 —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS013757 — — 10,071 individuals,
46.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013758 — — 10,071 individuals,
46.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013759 — — 10,071 individuals,
46.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013734 — — 8,059 individuals,
46.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013735 — — 8,059 individuals,
46.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013736 — — 8,059 individuals,
46.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013737 — — 8,059 individuals,
46.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013738 — — 8,059 individuals,
46.28 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013755 — — 10,071 individuals,
46.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013756 — — 10,071 individuals,
46.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —