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 term(s) 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 PGS 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
-
 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000702/ScoringFiles/PGS000702.txt.gz - Check Terms/Licenses

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 —

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
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 —
PSS000803 — — 2,058 individuals — European Participants self-identifying as white MESA —