Trait: Varicose veins

Trait Information
Identifier HP_0002619
Description Enlarged and tortuous veins. [HPO: probinson]
Trait category
Other trait
Mapped terms 8 mapped terms
  • DOID:799
  • ICD10:I83
  • ICD10:I86
  • MSH:D014648
  • SNOMEDCT_US:128060009
  • SNOMEDCT_US:12856003
  • SNOMEDCT_US:399989005
  • UMLS:C0042345

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)
PGS000937
(GBE_HC401)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Varicose veins Varicose veins 2,603
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000937/ScoringFiles/PGS000937.txt.gz
PGS000938
(GBE_HC990)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Varicose veins of lower extremities (time-to-event) Varicose veins 2,563
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000938/ScoringFiles/PGS000938.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
PPM007521 PGS000938
(GBE_HC990)
PSS004765|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE varicose veins of lower extremities AUROC: 0.64564 [0.63595, 0.65534] : 0.03681
Incremental AUROC (full-covars): 0.05082
PGS R2 (no covariates): 0.02091
PGS AUROC (no covariates): 0.61143 [0.60132, 0.62154]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007520 PGS000938
(GBE_HC990)
PSS004764|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE varicose veins of lower extremities AUROC: 0.67693 [0.64508, 0.70878] : 0.04959
Incremental AUROC (full-covars): 0.02832
PGS R2 (no covariates): 0.01507
PGS AUROC (no covariates): 0.59602 [0.56097, 0.63107]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007519 PGS000938
(GBE_HC990)
PSS004763|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE varicose veins of lower extremities AUROC: 0.65961 [0.6439, 0.67533] : 0.04514
Incremental AUROC (full-covars): 0.02733
PGS R2 (no covariates): 0.01623
PGS AUROC (no covariates): 0.59749 [0.58043, 0.61455]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007518 PGS000938
(GBE_HC990)
PSS004762|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE varicose veins of lower extremities AUROC: 0.6963 [0.60332, 0.78927] : 0.06309
Incremental AUROC (full-covars): 0.06018
PGS R2 (no covariates): 0.03496
PGS AUROC (no covariates): 0.64663 [0.54765, 0.7456]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007517 PGS000938
(GBE_HC990)
PSS004761|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE varicose veins of lower extremities AUROC: 0.62136 [0.57332, 0.6694] : 0.02314
Incremental AUROC (full-covars): -0.00473
PGS R2 (no covariates): 0.00107
PGS AUROC (no covariates): 0.52967 [0.4753, 0.58404]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007516 PGS000937
(GBE_HC401)
PSS004480|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Varicose veins AUROC: 0.63516 [0.62363, 0.64669] : 0.02861
Incremental AUROC (full-covars): 0.05484
PGS R2 (no covariates): 0.01871
PGS AUROC (no covariates): 0.60775 [0.59597, 0.61953]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007515 PGS000937
(GBE_HC401)
PSS004479|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Varicose veins AUROC: 0.67258 [0.63464, 0.71052] : 0.04734
Incremental AUROC (full-covars): 0.02962
PGS R2 (no covariates): 0.01842
PGS AUROC (no covariates): 0.60625 [0.56528, 0.64722]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007514 PGS000937
(GBE_HC401)
PSS004478|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Varicose veins AUROC: 0.65191 [0.63315, 0.67067] : 0.0371
Incremental AUROC (full-covars): 0.03634
PGS R2 (no covariates): 0.01715
PGS AUROC (no covariates): 0.60589 [0.58649, 0.62529]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007513 PGS000937
(GBE_HC401)
PSS004477|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Varicose veins AUROC: 0.71088 [0.62204, 0.79971] : 0.07134
Incremental AUROC (full-covars): 0.04391
PGS R2 (no covariates): 0.01451
PGS AUROC (no covariates): 0.60481 [0.48689, 0.72274]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007512 PGS000937
(GBE_HC401)
PSS004476|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Varicose veins AUROC: 0.59208 [0.53676, 0.64739] : 0.01447
Incremental AUROC (full-covars): -0.02413
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.49013 [0.43623, 0.54403]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004764
[
  • 253 cases
  • , 7,578 controls
]
South Asian UKB
PSS004765
[
  • 3,056 cases
  • , 64,369 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004478
[
  • 819 cases
  • , 24,086 controls
]
European non-white British ancestry UKB
PSS004479
[
  • 172 cases
  • , 7,659 controls
]
South Asian UKB
PSS004480
[
  • 2,219 cases
  • , 65,206 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004477
[
  • 25 cases
  • , 1,679 controls
]
East Asian UKB
PSS004476
[
  • 107 cases
  • , 6,390 controls
]
African unspecified UKB
PSS004761
[
  • 122 cases
  • , 6,375 controls
]
African unspecified UKB
PSS004762
[
  • 31 cases
  • , 1,673 controls
]
East Asian UKB
PSS004763
[
  • 1,101 cases
  • , 23,804 controls
]
European non-white British ancestry UKB