Trait: Hypercholesterolemia

Trait Information
Identifier HP_0003124
Description An increased concentration of cholesterol in the blood. [HPO: gcarletti]
Trait category
Other trait
Synonyms 3 synonyms
  • Elevated serum cholesterol
  • Elevated total cholesterol
  • Increased total cholesterol
Mapped terms 7 mapped terms
  • MSH:D006937
  • 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
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000936
(GBE_HC269)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
High cholesterol Hypercholesterolemia 5,987
-
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 cholesterol Hypercholesterolemia 1,109,311
-
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 cholesterol Hypercholesterolemia 3,246
-
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 cholesterol Hypercholesterolemia 13,788
-
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 cholesterol Hypercholesterolemia 90,341
-
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 cholesterol Hypercholesterolemia 810
-
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 cholesterol Hypercholesterolemia 545
-
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 cholesterol Hypercholesterolemia 195,463
-
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 cholesterol Hypercholesterolemia 937,601
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002700/ScoringFiles/PGS002700.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
PPM007507 PGS000936
(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] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007508 PGS000936
(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] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007509 PGS000936
(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] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007510 PGS000936
(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] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007511 PGS000936
(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] : 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 PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM013099 PGS002334
(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): 0.0063 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013148 PGS002334
(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): 0.0085 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013197 PGS002334
(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): 0.0225 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013246 PGS002334
(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): 0.0171 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013387 PGS002406
(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): 0.0001 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013436 PGS002406
(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): 0.0058 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013485 PGS002406
(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): 0.0033 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013534 PGS002406
(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): 0.005 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013583 PGS002455
(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): 0.0 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013632 PGS002455
(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): 0.0026 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013681 PGS002455
(disease_HI_CHOL_SELF_REP.P+T.0.001)
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): 0.0032 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013730 PGS002455
(disease_HI_CHOL_SELF_REP.P+T.0.001)
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): 0.0023 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013828 PGS002504
(disease_HI_CHOL_SELF_REP.P+T.0.01)
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): 0.0008 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013779 PGS002504
(disease_HI_CHOL_SELF_REP.P+T.0.01)
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): 0.0 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013877 PGS002504
(disease_HI_CHOL_SELF_REP.P+T.0.01)
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): 0.0015 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013926 PGS002504
(disease_HI_CHOL_SELF_REP.P+T.0.01)
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): 0.0006 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM013975 PGS002553
(disease_HI_CHOL_SELF_REP.P+T.1e-06)
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): 0.0002 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014024 PGS002553
(disease_HI_CHOL_SELF_REP.P+T.1e-06)
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): 0.0003 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014073 PGS002553
(disease_HI_CHOL_SELF_REP.P+T.1e-06)
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): 0.0118 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014122 PGS002553
(disease_HI_CHOL_SELF_REP.P+T.1e-06)
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): 0.0079 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014171 PGS002602
(disease_HI_CHOL_SELF_REP.P+T.5e-08)
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): 0.0018 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014220 PGS002602
(disease_HI_CHOL_SELF_REP.P+T.5e-08)
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): 0.0003 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014269 PGS002602
(disease_HI_CHOL_SELF_REP.P+T.5e-08)
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): 0.0115 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014318 PGS002602
(disease_HI_CHOL_SELF_REP.P+T.5e-08)
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): 0.0079 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014465 PGS002651
(disease_HI_CHOL_SELF_REP.PolyFun-pred)
PSS009781|
European Ancestry|
43,505 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0213 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs See disease_HI_CHOL_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014367 PGS002651
(disease_HI_CHOL_SELF_REP.PolyFun-pred)
PSS009779|
African Ancestry|
6,503 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0077 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs See disease_HI_CHOL_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014416 PGS002651
(disease_HI_CHOL_SELF_REP.PolyFun-pred)
PSS009780|
East Asian Ancestry|
922 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0103 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs See disease_HI_CHOL_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014514 PGS002651
(disease_HI_CHOL_SELF_REP.PolyFun-pred)
PSS009782|
South Asian Ancestry|
8,098 individuals
PGP000332 |
Weissbrod O et al. Nat Genet (2022)
Reported Trait: High cholesterol Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0193 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs See disease_HI_CHOL_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014563 PGS002700
(disease_HI_CHOL_SELF_REP.SBayesR)
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): 0.0085 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014612 PGS002700
(disease_HI_CHOL_SELF_REP.SBayesR)
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): 0.0065 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014661 PGS002700
(disease_HI_CHOL_SELF_REP.SBayesR)
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): 0.0213 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs
PPM014710 PGS002700
(disease_HI_CHOL_SELF_REP.SBayesR)
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): 0.0183 age, sex, age‚age*sex, assessment center, genotyping array, 10 PCs

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
PSS009779 6,503 individuals African unspecified UKB
PSS009780 922 individuals East Asian UKB
PSS009781 43,505 individuals European Non-British European UKB
PSS009782 8,098 individuals South Asian UKB
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
]
European non-white British ancestry UKB
PSS004397
[
  • 1,551 cases
  • , 6,280 controls
]
South Asian UKB
PSS004398
[
  • 8,999 cases
  • , 58,426 controls
]
European white British ancestry UKB Testing cohort (heldout set)