Trait: Thrombophlebitis

Trait Information
Identifier HP_0004418
Description Inflammation of a vein associated with venous thrombosis (blood clot formation within the vein). [HPO: probinson]
Trait category
Other trait
Mapped terms 3 mapped terms
  • MSH:D013924
  • SNOMEDCT_US:64156001
  • UMLS:C0040046

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)
PGS000961
(GBE_HC987)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Phlebitis and thrombophlebitis (time-to-event) Phlebitis,
Thrombophlebitis
1,143
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000961/ScoringFiles/PGS000961.txt.gz
PGS001844
(portability-PLR_451)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Phlebitis and thrombophlebitis Phlebitis,
Thrombophlebitis
431
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001844/ScoringFiles/PGS001844.txt.gz
PGS002056
(portability-ldpred2_451)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Phlebitis and thrombophlebitis Phlebitis,
Thrombophlebitis
114,679
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002056/ScoringFiles/PGS002056.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
PPM007629 PGS000961
(GBE_HC987)
PSS004756|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE phlebitis and thrombophlebitis AUROC: 0.63235 [0.59259, 0.67211] : 0.02507
Incremental AUROC (full-covars): 0.00771
PGS R2 (no covariates): 0.00171
PGS AUROC (no covariates): 0.53507 [0.4917, 0.57844]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007630 PGS000961
(GBE_HC987)
PSS004757|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE phlebitis and thrombophlebitis AUROC: 0.66631 [0.52571, 0.80691] : 0.04004
Incremental AUROC (full-covars): -0.006
PGS R2 (no covariates): 4e-05
PGS AUROC (no covariates): 0.50807 [0.37643, 0.63972]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007631 PGS000961
(GBE_HC987)
PSS004758|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE phlebitis and thrombophlebitis AUROC: 0.66949 [0.64981, 0.68916] : 0.04365
Incremental AUROC (full-covars): 0.03126
PGS R2 (no covariates): 0.01428
PGS AUROC (no covariates): 0.59647 [0.57489, 0.61804]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007632 PGS000961
(GBE_HC987)
PSS004759|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE phlebitis and thrombophlebitis AUROC: 0.63064 [0.58623, 0.67504] : 0.02362
Incremental AUROC (full-covars): 0.00728
PGS R2 (no covariates): 0.0042
PGS AUROC (no covariates): 0.55251 [0.5057, 0.59933]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007633 PGS000961
(GBE_HC987)
PSS004760|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE phlebitis and thrombophlebitis AUROC: 0.64191 [0.63056, 0.65326] : 0.03444
Incremental AUROC (full-covars): 0.03745
PGS R2 (no covariates): 0.01698
PGS AUROC (no covariates): 0.58931 [0.57719, 0.60143]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009642 PGS001844
(portability-PLR_451)
PSS009319|
European Ancestry|
18,164 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0525 [0.038, 0.067] sex, age, birth date, deprivation index, 16 PCs
PPM009643 PGS001844
(portability-PLR_451)
PSS009093|
European Ancestry|
3,734 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.068 [0.036, 0.1] sex, age, birth date, deprivation index, 16 PCs
PPM009644 PGS001844
(portability-PLR_451)
PSS008647|
European Ancestry|
6,014 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0468 [0.0215, 0.072] sex, age, birth date, deprivation index, 16 PCs
PPM009645 PGS001844
(portability-PLR_451)
PSS008421|
Greater Middle Eastern Ancestry|
1,102 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0855 [0.0261, 0.1444] sex, age, birth date, deprivation index, 16 PCs
PPM009646 PGS001844
(portability-PLR_451)
PSS008201|
South Asian Ancestry|
5,719 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0329 [0.0069, 0.0588] sex, age, birth date, deprivation index, 16 PCs
PPM009647 PGS001844
(portability-PLR_451)
PSS007983|
East Asian Ancestry|
1,622 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): -0.0182 [-0.0671, 0.0308] sex, age, birth date, deprivation index, 16 PCs
PPM009648 PGS001844
(portability-PLR_451)
PSS007766|
African Ancestry|
2,283 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0073 [-0.0339, 0.0485] sex, age, birth date, deprivation index, 16 PCs
PPM009649 PGS001844
(portability-PLR_451)
PSS008870|
African Ancestry|
3,611 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): -0.0032 [-0.0359, 0.0295] sex, age, birth date, deprivation index, 16 PCs
PPM011310 PGS002056
(portability-ldpred2_451)
PSS009319|
European Ancestry|
18,164 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0561 [0.0416, 0.0706] sex, age, birth date, deprivation index, 16 PCs
PPM011311 PGS002056
(portability-ldpred2_451)
PSS009093|
European Ancestry|
3,734 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0729 [0.0408, 0.1048] sex, age, birth date, deprivation index, 16 PCs
PPM011312 PGS002056
(portability-ldpred2_451)
PSS008647|
European Ancestry|
6,014 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0469 [0.0216, 0.0722] sex, age, birth date, deprivation index, 16 PCs
PPM011313 PGS002056
(portability-ldpred2_451)
PSS008421|
Greater Middle Eastern Ancestry|
1,102 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.085 [0.0256, 0.1439] sex, age, birth date, deprivation index, 16 PCs
PPM011314 PGS002056
(portability-ldpred2_451)
PSS008201|
South Asian Ancestry|
5,719 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): 0.0284 [0.0025, 0.0543] sex, age, birth date, deprivation index, 16 PCs
PPM011315 PGS002056
(portability-ldpred2_451)
PSS007983|
East Asian Ancestry|
1,622 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): -0.0188 [-0.0677, 0.0302] sex, age, birth date, deprivation index, 16 PCs
PPM011316 PGS002056
(portability-ldpred2_451)
PSS007766|
African Ancestry|
2,283 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): -0.001 [-0.0422, 0.0402] sex, age, birth date, deprivation index, 16 PCs
PPM011317 PGS002056
(portability-ldpred2_451)
PSS008870|
African Ancestry|
3,611 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Phlebitis and thrombophlebitis Partial Correlation (partial-r): -0.0043 [-0.037, 0.0284] 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
PSS009093 3,734 individuals European Poland (NE Europe) UKB
PSS008421 1,102 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009319 18,164 individuals European UK (+ Ireland) UKB
PSS008647 6,014 individuals European Italy (South Europe) UKB
PSS008201 5,719 individuals South Asian India (South Asia) UKB
PSS008870 3,611 individuals African unspecified Nigeria (West Africa) UKB
PSS007983 1,622 individuals East Asian China (East Asia) UKB
PSS007766 2,283 individuals African American or Afro-Caribbean Carribean UKB
PSS004756
[
  • 173 cases
  • , 6,324 controls
]
African unspecified UKB
PSS004757
[
  • 15 cases
  • , 1,689 controls
]
East Asian UKB
PSS004758
[
  • 710 cases
  • , 24,195 controls
]
European non-white British ancestry UKB
PSS004759
[
  • 145 cases
  • , 7,686 controls
]
South Asian UKB
PSS004760
[
  • 2,312 cases
  • , 65,113 controls
]
European white British ancestry UKB Testing cohort (heldout set)