Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_0004631 |
Description | A quantification of Vitamin D levels, typically in blood. Vitamin D includes both CHOLECALCIFEROLS and ERGOCALCIFEROLS, which have the common effect of preventing or curing RICKETS in animals. It can also be viewed as a hormone since it can be formed in SKIN by action of ULTRAVIOLET RAYS upon the precursors, 7-dehydrocholesterol and ERGOSTEROL, and acts on VITAMIN D RECEPTORS to regulate CALCIUM in opposition to PARATHYROID HORMONE (MeSH). 25-hydroxyvitamin D or calcifediol, a prehormone precursor of vitamin D, is widely used as a proxy to quanitfy vitamin D levels in blood. | Trait category |
Other measurement
|
Mapped terms |
2 mapped terms
|
Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS000702 (snpnet.Vitamin_D) |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Vitamin D [nmol/L] | vitamin D measurement | 8,012 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000702/ScoringFiles/PGS000702.txt.gz |
PGS000882 (25OHD_SBayesR_PGS) |
PGP000228 | Revez JA et al. Nat Commun (2020) |
25-hydroxyvitamin D | vitamin D measurement | 1,094,650 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000882/ScoringFiles/PGS000882.txt.gz |
PGS001982 (portability-PLR_log_vitaminD) |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Vitamin D | vitamin D measurement | 35,123 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001982/ScoringFiles/PGS001982.txt.gz |
PGS002200 (portability-ldpred2_log_vitaminD) |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Vitamin D | vitamin D measurement | 567,735 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002200/ScoringFiles/PGS002200.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 |
---|---|---|---|---|---|---|---|---|---|
PPM001430 | PGS000702 (snpnet.Vitamin_D) |
PSS000787| African Ancestry| 5,845 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Vitamin D [nmol/L] | — | — | R²: 0.09201 Spearman's ρ: 0.055 |
Age, sex, PCs(1-40) | — |
PPM001465 | PGS000702 (snpnet.Vitamin_D) |
PSS000788| East Asian Ancestry| 1,055 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Vitamin D [nmol/L] | — | — | R²: 0.11925 Spearman's ρ: 0.095 |
Age, sex, PCs(1-40) | — |
PPM001500 | PGS000702 (snpnet.Vitamin_D) |
PSS000789| European Ancestry| 22,617 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Vitamin D [nmol/L] | — | — | R²: 0.21171 Spearman's ρ: 0.211 |
Age, sex, PCs(1-40) | — |
PPM001535 | PGS000702 (snpnet.Vitamin_D) |
PSS000790| South Asian Ancestry| 6,425 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Vitamin D [nmol/L] | — | — | R²: 0.07695 Spearman's ρ: 0.08 |
Age, sex, PCs(1-40) | — |
PPM001570 | PGS000702 (snpnet.Vitamin_D) |
PSS000791| European Ancestry| 60,998 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Vitamin D [nmol/L] | — | — | R²: 0.22856 Spearman's ρ: 0.226 |
Age, sex, PCs(1-40) | — |
PPM001586 | PGS000702 (snpnet.Vitamin_D) |
PSS000803| European Ancestry| 2,058 individuals |
PGP000128 | Sinnott-Armstrong N et al. Nat Genet (2021) |
Reported Trait: Vitamin D [nmol/L] | — | — | Spearman's ρ: 0.137 | Age, sex | — |
PPM007435 | PGS000702 (snpnet.Vitamin_D) |
PSS007216| African Ancestry| 5,926 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Vitamin D | — | — | R²: 0.04539 [0.0355, 0.05527] Incremental R2 (full-covars): 0.00047 PGS R2 (no covariates): 0.00322 [0.00047, 0.00597] |
age, sex, UKB array type, Genotype PCs | — |
PPM007436 | PGS000702 (snpnet.Vitamin_D) |
PSS007217| East Asian Ancestry| 1,570 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Vitamin D | — | — | R²: 0.05891 [0.03726, 0.08055] Incremental R2 (full-covars): 0.00078 PGS R2 (no covariates): 0.00411 [-0.00194, 0.01016] |
age, sex, UKB array type, Genotype PCs | — |
PPM007437 | PGS000702 (snpnet.Vitamin_D) |
PSS007218| European Ancestry| 22,820 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Vitamin D | — | — | R²: 0.01597 [0.01288, 0.01905] Incremental R2 (full-covars): 0.0019 PGS R2 (no covariates): 0.04772 [0.04255, 0.05289] |
age, sex, UKB array type, Genotype PCs | — |
PPM007438 | PGS000702 (snpnet.Vitamin_D) |
PSS007219| South Asian Ancestry| 6,507 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Vitamin D | — | — | R²: 0.05098 [0.04149, 0.06047] Incremental R2 (full-covars): 0.00081 PGS R2 (no covariates): 0.00364 [0.00098, 0.00631] |
age, sex, UKB array type, Genotype PCs | — |
PPM007439 | PGS000702 (snpnet.Vitamin_D) |
PSS007220| European Ancestry| 61,724 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |Ext. |
Reported Trait: Vitamin D | — | — | R²: 0.01125 [0.00967, 0.01283] Incremental R2 (full-covars): 0.00186 PGS R2 (no covariates): 0.0483 [0.04514, 0.05145] |
age, sex, UKB array type, Genotype PCs | — |
PPM002526 | PGS000882 (25OHD_SBayesR_PGS) |
PSS001141| European Ancestry| 1,632 individuals |
PGP000228 | Revez JA et al. Nat Commun (2020) |
Reported Trait: 25-hydroxyvitamin D levels | β: 0.269 (0.02) | — | R²: 0.096 | sex, assessment month, supplement intake (ever), PCs(1-5) | — |
PPM002527 | PGS000882 (25OHD_SBayesR_PGS) |
PSS001142| European Ancestry| 1,632 individuals |
PGP000228 | Revez JA et al. Nat Commun (2020) |
Reported Trait: 25-hydroxyvitamin D levels | β: 0.24 (0.024) | — | R²: 0.0554 | — | — |
PPM010731 | PGS001982 (portability-PLR_log_vitaminD) |
PSS009470| European Ancestry| 18,172 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.2293 [0.2154, 0.243] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM010732 | PGS001982 (portability-PLR_log_vitaminD) |
PSS009244| European Ancestry| 3,778 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.1838 [0.1527, 0.2145] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM010733 | PGS001982 (portability-PLR_log_vitaminD) |
PSS008798| European Ancestry| 6,046 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.2179 [0.1937, 0.2418] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM010734 | PGS001982 (portability-PLR_log_vitaminD) |
PSS008572| Greater Middle Eastern Ancestry| 1,036 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.1893 [0.1293, 0.2479] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM010735 | PGS001982 (portability-PLR_log_vitaminD) |
PSS008350| South Asian Ancestry| 5,186 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.0774 [0.0502, 0.1044] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM010736 | PGS001982 (portability-PLR_log_vitaminD) |
PSS008127| East Asian Ancestry| 1,662 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.081 [0.0327, 0.1289] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM010738 | PGS001982 (portability-PLR_log_vitaminD) |
PSS009018| African Ancestry| 3,569 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.0393 [0.0064, 0.0721] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM010737 | PGS001982 (portability-PLR_log_vitaminD) |
PSS007914| African Ancestry| 2,266 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.0616 [0.0203, 0.1027] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM012447 | PGS002200 (portability-ldpred2_log_vitaminD) |
PSS009470| European Ancestry| 18,172 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.2228 [0.2089, 0.2365] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM012448 | PGS002200 (portability-ldpred2_log_vitaminD) |
PSS009244| European Ancestry| 3,778 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.174 [0.1428, 0.2048] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM012449 | PGS002200 (portability-ldpred2_log_vitaminD) |
PSS008798| European Ancestry| 6,046 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.2231 [0.199, 0.247] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM012450 | PGS002200 (portability-ldpred2_log_vitaminD) |
PSS008572| Greater Middle Eastern Ancestry| 1,036 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.1892 [0.1292, 0.2478] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM012452 | PGS002200 (portability-ldpred2_log_vitaminD) |
PSS008127| East Asian Ancestry| 1,662 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.084 [0.0358, 0.1319] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM012453 | PGS002200 (portability-ldpred2_log_vitaminD) |
PSS007914| African Ancestry| 2,266 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.0669 [0.0256, 0.1079] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM012454 | PGS002200 (portability-ldpred2_log_vitaminD) |
PSS009018| African Ancestry| 3,569 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.0423 [0.0094, 0.0751] | sex, age, birth date, deprivation index, 16 PCs | — |
PPM012451 | PGS002200 (portability-ldpred2_log_vitaminD) |
PSS008350| South Asian Ancestry| 5,186 individuals |
PGP000263 | Privé F et al. Am J Hum Genet (2022) |
Reported Trait: Vitamin D | — | — | Partial Correlation (partial-r): 0.0828 [0.0557, 0.1098] | sex, age, birth date, deprivation index, 16 PCs | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS001141 | — | — | 1,632 individuals | — | European | — | QIMR | — |
PSS001142 | — | — | 1,632 individuals | — | European | — | UKB | — |
PSS008798 | — | — | 6,046 individuals | — | European | Italy (South Europe) | UKB | — |
PSS007914 | — | — | 2,266 individuals | — | African American or Afro-Caribbean | Carribean | UKB | — |
PSS008572 | — | — | 1,036 individuals | — | Greater Middle Eastern (Middle Eastern, North African or Persian) | Iran (Middle East) | UKB | — |
PSS009470 | — | — | 18,172 individuals | — | European | UK (+ Ireland) | UKB | — |
PSS009244 | — | — | 3,778 individuals | — | European | Poland (NE Europe) | UKB | — |
PSS008350 | — | — | 5,186 individuals | — | South Asian | India (South Asia) | UKB | — |
PSS000787 | — | — | 5,845 individuals | — | African unspecified | — | UKB | — |
PSS000788 | — | — | 1,055 individuals | — | East Asian | — | UKB | — |
PSS000789 | — | — | 22,617 individuals | — | European | Non-British White | UKB | — |
PSS000790 | — | — | 6,425 individuals | — | South Asian | — | UKB | — |
PSS000791 | — | — | 60,998 individuals | — | European (British) |
— | UKB | — |
PSS007216 | — | — | 5,926 individuals | — | African unspecified | — | UKB | — |
PSS007217 | — | — | 1,570 individuals | — | East Asian | — | UKB | — |
PSS007218 | — | — | 22,820 individuals | — | European | non-white British ancestry | UKB | — |
PSS007219 | — | — | 6,507 individuals | — | South Asian | — | UKB | — |
PSS007220 | — | — | 61,724 individuals | — | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS009018 | — | — | 3,569 individuals | — | African unspecified | Nigeria (West Africa) | UKB | — |
PSS008127 | — | — | 1,662 individuals | — | East Asian | China (East Asia) | UKB | — |
PSS000803 | — | — | 2,058 individuals | — | European | Participants self-identifying as white | MESA | — |