Trait: vitamin B12 measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004620
Description is a quantification of Vitamin B12, vitamin B12 or vitamin B-12, is a water-solublevitamin with a key role in the normal functioning of the brain and nervous system, and for the formation of blood. It is one of the eight B vitamins. It is normally involved in themetabolism of every cell of the human body, especially affecting DNA synthesis and regulation, but also fatty acid synthesis and energy production. It is the largest and most structurally complicated vitamin and can be produced industrially only through bacterial fermentation-synthesis.
Trait category
Other measurement
Synonym vitamin B12 levels
Mapped terms 2 mapped terms
  • NCIt:C64817
  • SNOMEDCT:14598005

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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS003154
(ExPRSweb_VitB12_100013-irnt_LASSOSUM_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 314,838
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003154/ScoringFiles/PGS003154.txt.gz
PGS003155
(ExPRSweb_VitB12_100013-irnt_PT_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 40,176
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003155/ScoringFiles/PGS003155.txt.gz
PGS003156
(ExPRSweb_VitB12_100013-irnt_PLINK_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 88,908
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003156/ScoringFiles/PGS003156.txt.gz
PGS003157
(ExPRSweb_VitB12_100013-irnt_DBSLMM_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 10,318,270
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003157/ScoringFiles/PGS003157.txt.gz
PGS003158
(ExPRSweb_VitB12_100013-irnt_PRSCS_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 1,113,819
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003158/ScoringFiles/PGS003158.txt.gz
PGS003159
(ExPRSweb_VitB12_100013-raw_LASSOSUM_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 313,902
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003159/ScoringFiles/PGS003159.txt.gz
PGS003160
(ExPRSweb_VitB12_100013-raw_PT_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 83,714
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003160/ScoringFiles/PGS003160.txt.gz
PGS003161
(ExPRSweb_VitB12_100013-raw_PLINK_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 190,297
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003161/ScoringFiles/PGS003161.txt.gz
PGS003162
(ExPRSweb_VitB12_100013-raw_DBSLMM_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 10,318,272
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003162/ScoringFiles/PGS003162.txt.gz
PGS003163
(ExPRSweb_VitB12_100013-raw_PRSCS_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 1,113,819
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003163/ScoringFiles/PGS003163.txt.gz
PGS003164
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_LASSOSUM_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 263,612
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003164/ScoringFiles/PGS003164.txt.gz
PGS003165
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PT_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 9
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003165/ScoringFiles/PGS003165.txt.gz
PGS003166
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PLINK_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 9
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003166/ScoringFiles/PGS003166.txt.gz
PGS003167
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_DBSLMM_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 9,805
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003167/ScoringFiles/PGS003167.txt.gz
PGS003168
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PRSCS_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 1,100,788
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003168/ScoringFiles/PGS003168.txt.gz
PGS003169
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_LASSOSUM_UKB_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 291,530
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003169/ScoringFiles/PGS003169.txt.gz
PGS003170
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PT_UKB_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 2,232
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003170/ScoringFiles/PGS003170.txt.gz
PGS003171
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PLINK_UKB_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 2,232
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003171/ScoringFiles/PGS003171.txt.gz
PGS003172
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_DBSLMM_UKB_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 5,880
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003172/ScoringFiles/PGS003172.txt.gz
PGS003173
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PRSCS_UKB_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Vitamin B12 vitamin B12 measurement 1,101,425
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003173/ScoringFiles/PGS003173.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
PPM016058 PGS003154
(ExPRSweb_VitB12_100013-irnt_LASSOSUM_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 0.365 (3.88) — R²: 1.57e-08 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016061 PGS003155
(ExPRSweb_VitB12_100013-irnt_PT_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 0.866 (3.88) — R²: 4.89e-06 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016059 PGS003156
(ExPRSweb_VitB12_100013-irnt_PLINK_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 4.44 (3.92) — R²: 0.00028 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016057 PGS003157
(ExPRSweb_VitB12_100013-irnt_DBSLMM_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: -2.1 (3.88) — R²: 7e-05 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016060 PGS003158
(ExPRSweb_VitB12_100013-irnt_PRSCS_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: -0.43 (3.88) — R²: 4.00e-06 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016063 PGS003159
(ExPRSweb_VitB12_100013-raw_LASSOSUM_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 1.28 (3.82) — R²: 1e-05 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016066 PGS003160
(ExPRSweb_VitB12_100013-raw_PT_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: -0.723 (3.87) — R²: 2e-05 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016064 PGS003161
(ExPRSweb_VitB12_100013-raw_PLINK_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: -3.57 (3.82) — R²: 0.00022 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016062 PGS003162
(ExPRSweb_VitB12_100013-raw_DBSLMM_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: -1.78 (3.84) — R²: 5e-05 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016065 PGS003163
(ExPRSweb_VitB12_100013-raw_PRSCS_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 1.98 (3.9) — R²: 3e-05 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016069 PGS003164
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_LASSOSUM_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 12.0 (3.89) — R²: 0.00207 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016075 PGS003165
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PT_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 12.6 (3.87) — R²: 0.00237 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016071 PGS003166
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PLINK_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 12.6 (3.87) — R²: 0.00237 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016067 PGS003167
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_DBSLMM_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: -4.03 (3.85) — R²: 0.00025 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016073 PGS003168
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PRSCS_MGI_20211120)
 PSS010019|
European Ancestry|
4,313 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 6.06 (3.83) — R²: 0.00068 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —
PPM016070 PGS003169
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_LASSOSUM_UKB_20211120)
 PSS010035|
Ancestry Not Reported|
174,277 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 0.0193 (0.015) — R²: 2e-05 Sex,birthYear,genotyping.array,PC1,PC2,PC3,PC4 —
PPM016076 PGS003170
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PT_UKB_20211120)
 PSS010035|
Ancestry Not Reported|
174,277 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: -0.0115 (0.0144) — R²: 7.35e-06 Sex,birthYear,genotyping.array,PC1,PC2,PC3,PC4 —
PPM016072 PGS003171
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PLINK_UKB_20211120)
 PSS010035|
Ancestry Not Reported|
174,277 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: -0.0115 (0.0144) — R²: 7.35e-06 Sex,birthYear,genotyping.array,PC1,PC2,PC3,PC4 —
PPM016068 PGS003172
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_DBSLMM_UKB_20211120)
 PSS010035|
Ancestry Not Reported|
174,277 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: -0.00152 (0.015) — R²: 9.98e-07 Sex,birthYear,genotyping.array,PC1,PC2,PC3,PC4 —
PPM016074 PGS003173
(ExPRSweb_VitB12_Wood-et-al-2013-1000G_PRSCS_UKB_20211120)
 PSS010035|
Ancestry Not Reported|
174,277 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin B12 β: 0.00804 (0.015) — R²: 5.26e-06 Sex,birthYear,genotyping.array,PC1,PC2,PC3,PC4 —

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
PSS010019 VITAMIN B12 LEVEL (LOINC: 2132-9); Quantitative — 4,313 individuals — European — MGI —
PSS010035 — — 174,277 individuals — Not reported — UKB —