Trait: Varicose veins

Trait Information
Identifier HP_0002619
Description Enlarged and tortuous veins.
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
GWAS
Dev
Eval
 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
PGS004463
(disease.I83.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 I83 (Varicose veins of lower extremities) Varicose veins 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004463/ScoringFiles/PGS004463.txt.gz
PGS004533
(meta.I83.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 I83 (Varicose veins of lower extremities) Varicose veins 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004533/ScoringFiles/PGS004533.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
R²: 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] R²: 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] R²: 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] R²: 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] R²: 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] R²: 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] R²: 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] R²: 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] R²: 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] R²: 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 —
PPM020578 PGS004463
(disease.I83.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: I83 (Varicose veins of lower extremities) OR: 1.29902 — — — —
PPM020648 PGS004533
(meta.I83.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: I83 (Varicose veins of lower extremities) OR: 1.24767 — — — —

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
PSS008648 — — 6,131 individuals — European Italy (South Europe) UKB —
PSS007767 — — 2,295 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008422 — — 1,116 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009320 — — 18,550 individuals — European UK (+ Ireland) UKB —
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)
PSS009094 — — 3,835 individuals — European Poland (NE Europe) UKB —
PSS008202 — — 5,823 individuals — South Asian India (South Asia) UKB —
PSS011364 — — 56,192 individuals — European — 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 —
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)
PSS008871 — — 3,619 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007984 — — 1,639 individuals — East Asian China (East Asia) UKB —