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. PLoS Genet (2022)
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. PLoS Genet (2022)
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
PGS001845
(portability-PLR_454)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Varicose veins Varicose veins 15,748
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001845/ScoringFiles/PGS001845.txt.gz
PGS002057
(portability-ldpred2_454)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Varicose veins Varicose veins 760,630
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002057/ScoringFiles/PGS002057.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
PPM007512 PGS000937
(GBE_HC401)
PSS004476|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Varicose veins AUROC: 0.59208 [0.53676, 0.64739] PGS R2 (no covariates): 0.0
: 0.01447
Incremental AUROC (full-covars): -0.02413
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
PPM007513 PGS000937
(GBE_HC401)
PSS004477|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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
PPM007514 PGS000937
(GBE_HC401)
PSS004478|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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
PPM007515 PGS000937
(GBE_HC401)
PSS004479|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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
PPM007516 PGS000937
(GBE_HC401)
PSS004480|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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
PPM007517 PGS000938
(GBE_HC990)
PSS004761|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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
PPM007518 PGS000938
(GBE_HC990)
PSS004762|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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
PPM007519 PGS000938
(GBE_HC990)
PSS004763|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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
PPM007520 PGS000938
(GBE_HC990)
PSS004764|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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
PPM007521 PGS000938
(GBE_HC990)
PSS004765|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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
PPM009650 PGS001845
(portability-PLR_454)
PSS009320|
European Ancestry|
18,550 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0701 [0.0558, 0.0844] sex, age, birth date, deprivation index, 16 PCs
PPM009651 PGS001845
(portability-PLR_454)
PSS009094|
European Ancestry|
3,835 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0814 [0.0498, 0.1128] sex, age, birth date, deprivation index, 16 PCs
PPM009652 PGS001845
(portability-PLR_454)
PSS008648|
European Ancestry|
6,131 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0563 [0.0313, 0.0813] sex, age, birth date, deprivation index, 16 PCs
PPM009653 PGS001845
(portability-PLR_454)
PSS008422|
Greater Middle Eastern Ancestry|
1,116 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): -0.001 [-0.0602, 0.0582] sex, age, birth date, deprivation index, 16 PCs
PPM009654 PGS001845
(portability-PLR_454)
PSS008202|
South Asian Ancestry|
5,823 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0772 [0.0516, 0.1027] sex, age, birth date, deprivation index, 16 PCs
PPM009655 PGS001845
(portability-PLR_454)
PSS007984|
East Asian Ancestry|
1,639 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0882 [0.0397, 0.1364] sex, age, birth date, deprivation index, 16 PCs
PPM009656 PGS001845
(portability-PLR_454)
PSS007767|
African Ancestry|
2,295 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.001 [-0.0401, 0.0421] sex, age, birth date, deprivation index, 16 PCs
PPM009657 PGS001845
(portability-PLR_454)
PSS008871|
African Ancestry|
3,619 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0172 [-0.0155, 0.0498] sex, age, birth date, deprivation index, 16 PCs
PPM011318 PGS002057
(portability-ldpred2_454)
PSS009320|
European Ancestry|
18,550 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0824 [0.0681, 0.0967] sex, age, birth date, deprivation index, 16 PCs
PPM011319 PGS002057
(portability-ldpred2_454)
PSS009094|
European Ancestry|
3,835 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.083 [0.0514, 0.1145] sex, age, birth date, deprivation index, 16 PCs
PPM011320 PGS002057
(portability-ldpred2_454)
PSS008648|
European Ancestry|
6,131 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0666 [0.0416, 0.0915] sex, age, birth date, deprivation index, 16 PCs
PPM011321 PGS002057
(portability-ldpred2_454)
PSS008422|
Greater Middle Eastern Ancestry|
1,116 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): -0.0216 [-0.0807, 0.0377] sex, age, birth date, deprivation index, 16 PCs
PPM011322 PGS002057
(portability-ldpred2_454)
PSS008202|
South Asian Ancestry|
5,823 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0802 [0.0546, 0.1057] sex, age, birth date, deprivation index, 16 PCs
PPM011323 PGS002057
(portability-ldpred2_454)
PSS007984|
East Asian Ancestry|
1,639 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0953 [0.0468, 0.1434] sex, age, birth date, deprivation index, 16 PCs
PPM011324 PGS002057
(portability-ldpred2_454)
PSS007767|
African Ancestry|
2,295 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0038 [-0.0373, 0.0449] sex, age, birth date, deprivation index, 16 PCs
PPM011325 PGS002057
(portability-ldpred2_454)
PSS008871|
African Ancestry|
3,619 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Varicose veins Partial Correlation (partial-r): 0.0324 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
PSS004476
[
  • 107 cases
  • , 6,390 controls
]
African unspecified UKB
PSS004477
[
  • 25 cases
  • , 1,679 controls
]
East Asian UKB
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)
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)
PSS009320 18,550 individuals European UK (+ Ireland) UKB
PSS009094 3,835 individuals European Poland (NE Europe) UKB
PSS008648 6,131 individuals European Italy (South Europe) UKB
PSS008422 1,116 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008202 5,823 individuals South Asian India (South Asia) UKB
PSS007984 1,639 individuals East Asian China (East Asia) UKB
PSS008871 3,619 individuals African unspecified Nigeria (West Africa) UKB
PSS007767 2,295 individuals African American or Afro-Caribbean Carribean 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