Trait Information | |
Identifier | HP_0003124 |
Description | An increased concentration of cholesterol in the blood. [HPO_CONTRIBUTOR: gcarletti] | Trait category |
Other trait
|
Synonyms |
4 synonyms
|
Mapped terms |
6 mapped terms
|
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 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 |
PGS002764 (LDL_prscs) |
PGP000364 | Mars N et al. Am J Hum Genet (2022) |
Hypercholesterolemia | Hypercholesterolemia | 1,091,280 | - |
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) |
Hypercholesterolemia | Hypercholesterolemia | 975,107 | - |
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) |
Hypercholesterolemia | Hypercholesterolemia | 3,948,507 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004784/ScoringFiles/PGS004784.txt.gz |
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] | 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 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] | 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 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] | 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 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] | 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 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] | 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 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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*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*sex, assessment center, genotyping array, 10 PCs | — |
PPM014964 | PGS002764 (LDL_prscs) |
PSS009939| European Ancestry| 39,444 individuals |
PGP000364 | Mars N et al. Am J Hum Genet (2022) |
Reported Trait: Hypercholesterolemia | OR: 1.72 [1.67, 1.77] | — | — | age, sex, 10 PCs, technical covariates | — |
PPM021008 | PGS004783 (HLD_PRSmix_eur) |
PSS011465| European Ancestry| 9,462 individuals |
PGP000604 | Truong B et al. Cell Genom (2024) |
Reported Trait: Hypercholesterolemia | — | — | Incremental R2 (Full model versus model with only covariates): 0.041 [0.034, 0.049] | age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 | Incremental R2 (Full model versus model with only covariates) |
PPM021009 | PGS004784 (HLD_PRSmixPlus_eur) |
PSS011465| European Ancestry| 9,462 individuals |
PGP000604 | Truong B et al. Cell Genom (2024) |
Reported Trait: Hypercholesterolemia | — | — | Incremental R2 (Full model versus model with only covariates): 0.052 [0.043, 0.061] | age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 | Incremental R2 (Full model versus model with only covariates) |
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 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS004395 | — | — | [
|
— | East Asian | — | UKB | — |
PSS004396 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS004397 | — | — | [
|
— | South Asian | — | UKB | — |
PSS004398 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS011465 | — | — | 9,462 individuals | — | European | — | AllofUs | — |
PSS009939 | — | — | 39,444 individuals | — | European (Finnish) |
— | FinnGen | — |