Trait: vitamin D measurement

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
  • NCIt:C84818
  • SNOMEDCT:83729008

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)
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 - Check Terms/Licenses
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

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
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 —

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
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 —