Trait: Hypercholesterolemia

Trait Information
Identifier HP_0003124
Description An increased concentration of cholesterol in the blood. [HPO_CONTRIBUTOR: gcarletti]
Trait category
Other trait
Synonyms 4 synonyms
  • Elevated serum cholesterol
  • Elevated total cholesterol
  • High cholesterol
  • Increased total cholesterol
Mapped terms 6 mapped terms
  • NCIt:C37967
  • SNOMEDCT:13644009
  • SNOMEDCT_US:13644009
  • SNOMEDCT_US:166830008
  • UMLS:C0020443
  • UMLS:C0595929

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
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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)
PGS000936
(GBE_HC269)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
High cholesterolHypercholesterolemia5,987
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000936/ScoringFiles/PGS000936.txt.gz
PGS002334
(disease_HI_CHOL_SELF_REP.BOLT-LMM)
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
High cholesterolHypercholesterolemia1,109,311
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002334/ScoringFiles/PGS002334.txt.gz
PGS002406
(disease_HI_CHOL_SELF_REP.P+T.0.0001)
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
High cholesterolHypercholesterolemia3,246
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002406/ScoringFiles/PGS002406.txt.gz
PGS002455
(disease_HI_CHOL_SELF_REP.P+T.0.001)
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
High cholesterolHypercholesterolemia13,788
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002455/ScoringFiles/PGS002455.txt.gz
PGS002504
(disease_HI_CHOL_SELF_REP.P+T.0.01)
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
High cholesterolHypercholesterolemia90,341
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002504/ScoringFiles/PGS002504.txt.gz
PGS002553
(disease_HI_CHOL_SELF_REP.P+T.1e-06)
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
High cholesterolHypercholesterolemia810
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002553/ScoringFiles/PGS002553.txt.gz
PGS002602
(disease_HI_CHOL_SELF_REP.P+T.5e-08)
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
High cholesterolHypercholesterolemia545
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002602/ScoringFiles/PGS002602.txt.gz
PGS002651
(disease_HI_CHOL_SELF_REP.PolyFun-pred)
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
High cholesterolHypercholesterolemia195,463
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002651/ScoringFiles/PGS002651.txt.gz
PGS002700
(disease_HI_CHOL_SELF_REP.SBayesR)
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
High cholesterolHypercholesterolemia937,601
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002700/ScoringFiles/PGS002700.txt.gz
PGS002764
(LDL_prscs)
PGP000364 |
Mars N et al. Am J Hum Genet (2022)
HypercholesterolemiaHypercholesterolemia1,091,280
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002764/ScoringFiles/PGS002764.txt.gz
PGS004783
(HLD_PRSmix_eur)
PGP000604 |
Truong B et al. Cell Genom (2024)
HypercholesterolemiaHypercholesterolemia975,107
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004783/ScoringFiles/PGS004783.txt.gz
PGS004784
(HLD_PRSmixPlus_eur)
PGP000604 |
Truong B et al. Cell Genom (2024)
HypercholesterolemiaHypercholesterolemia3,948,507
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004784/ScoringFiles/PGS004784.txt.gz
Showing 1 to 12 of 12 rows

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.

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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
PPM007507PGS000936
(GBE_HC269)
PSS004394|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: High cholesterol—AUROC: 0.71982 [0.7005, 0.73913]R²: 0.11508
Incremental AUROC (full-covars): 0.00533
PGS R2 (no covariates): 0.00875
PGS AUROC (no covariates): 0.55909 [0.53701, 0.58116]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007508PGS000936
(GBE_HC269)
PSS004395|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: High cholesterol—AUROC: 0.72115 [0.67901, 0.76329]R²: 0.11225
Incremental AUROC (full-covars): 0.01895
PGS R2 (no covariates): 0.01737
PGS AUROC (no covariates): 0.58299 [0.53527, 0.6307]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007509PGS000936
(GBE_HC269)
PSS004396|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: High cholesterol—AUROC: 0.73677 [0.72785, 0.7457]R²: 0.1386
Incremental AUROC (full-covars): 0.03212
PGS R2 (no covariates): 0.03624
PGS AUROC (no covariates): 0.62158 [0.61091, 0.63225]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007510PGS000936
(GBE_HC269)
PSS004397|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: High cholesterol—AUROC: 0.68493 [0.67098, 0.69888]R²: 0.10135
Incremental AUROC (full-covars): 0.01608
PGS R2 (no covariates): 0.01913
PGS AUROC (no covariates): 0.57791 [0.56213, 0.5937]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007511PGS000936
(GBE_HC269)
PSS004398|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: High cholesterol—AUROC: 0.72791 [0.72273, 0.73309]R²: 0.13664
Incremental AUROC (full-covars): 0.03518
PGS R2 (no covariates): 0.03794
PGS AUROC (no covariates): 0.61972 [0.6136, 0.62583]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM013099PGS002334
(disease_HI_CHOL_SELF_REP.BOLT-LMM)
PSS009779|
African Ancestry|
6,503 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol——Incremental R2 (full model vs. covariates alone): 0.0063age, sex, age*sex, assessment center, genotyping array, 10 PCs—
PPM013148PGS002334
(disease_HI_CHOL_SELF_REP.BOLT-LMM)
PSS009780|
East Asian Ancestry|
922 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol——Incremental R2 (full model vs. covariates alone): 0.0085age, sex, age*sex, assessment center, genotyping array, 10 PCs—
PPM013197PGS002334
(disease_HI_CHOL_SELF_REP.BOLT-LMM)
PSS009781|
European Ancestry|
43,505 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol——Incremental R2 (full model vs. covariates alone): 0.0225age, sex, age*sex, assessment center, genotyping array, 10 PCs—
PPM013246PGS002334
(disease_HI_CHOL_SELF_REP.BOLT-LMM)
PSS009782|
South Asian Ancestry|
8,098 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol——Incremental R2 (full model vs. covariates alone): 0.0171age, sex, age*sex, assessment center, genotyping array, 10 PCs—
PPM013387PGS002406
(disease_HI_CHOL_SELF_REP.P+T.0.0001)
PSS009779|
African Ancestry|
6,503 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol——Incremental R2 (full model vs. covariates alone): 0.0001age, sex, age*sex, assessment center, genotyping array, 10 PCs—
PPM013436PGS002406
(disease_HI_CHOL_SELF_REP.P+T.0.0001)
PSS009780|
East Asian Ancestry|
922 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol——Incremental R2 (full model vs. covariates alone): 0.0058age, sex, age*sex, assessment center, genotyping array, 10 PCs—
PPM013485PGS002406
(disease_HI_CHOL_SELF_REP.P+T.0.0001)
PSS009781|
European Ancestry|
43,505 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol——Incremental R2 (full model vs. covariates alone): 0.0033age, sex, age*sex, assessment center, genotyping array, 10 PCs—
PPM013534PGS002406
(disease_HI_CHOL_SELF_REP.P+T.0.0001)
PSS009782|
South Asian Ancestry|
8,098 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol——Incremental R2 (full model vs. covariates alone): 0.005age, sex, age*sex, assessment center, genotyping array, 10 PCs—
PPM013583PGS002455
(disease_HI_CHOL_SELF_REP.P+T.0.001)
PSS009779|
African Ancestry|
6,503 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol——Incremental R2 (full model vs. covariates alone): 0.0age, sex, age*sex, assessment center, genotyping array, 10 PCs—
PPM013632PGS002455
(disease_HI_CHOL_SELF_REP.P+T.0.001)
PSS009780|
East Asian Ancestry|
922 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol——Incremental R2 (full model vs. covariates alone): 0.0026age, sex, age*sex, assessment center, genotyping array, 10 PCs—
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Evaluated Samples

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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
PSS004394——
[
  • 718 cases
  • , 5,779 controls
]
—African unspecified—UKB—
PSS004395——
[
  • 164 cases
  • , 1,540 controls
]
—East Asian—UKB—
PSS004396——
[
  • 2,910 cases
  • , 21,995 controls
]
—Europeannon-white British ancestryUKB—
PSS004397——
[
  • 1,551 cases
  • , 6,280 controls
]
—South Asian—UKB—
PSS004398——
[
  • 8,999 cases
  • , 58,426 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
PSS009779——6,503 individuals—African unspecified—UKB—
PSS009780——922 individuals—East Asian—UKB—
PSS009781——43,505 individuals—EuropeanNon-British EuropeanUKB—
PSS009782——8,098 individuals—South Asian—UKB—
PSS009939——39,444 individuals—European
(Finnish)		—FinnGen—
PSS011465——9,462 individuals—European—AllofUs—
Showing 1 to 11 of 11 rows