Trait: Cholecystitis

Trait Information
Identifier HP_0001082
Description The presence of inflammatory changes in the gallbladder.
Trait category
Other trait
Synonym Gallbladder inflammation
Mapped terms 3 mapped terms
  • ICD10:K81
  • SNOMEDCT_US:76581006
  • UMLS:C0008325

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)
PGS000707
(HC225)
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Cholecystitis Cholecystitis 183,329
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000707/ScoringFiles/PGS000707.txt.gz - Check Terms/Licenses
PGS000942
(GBE_HC225)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Cholecystitis Cholecystitis 391
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000942/ScoringFiles/PGS000942.txt.gz
PGS000943
(GBE_HC1126)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Cholecystitis (time-to-event) Cholecystitis 5
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000943/ScoringFiles/PGS000943.txt.gz
PGS001861
(portability-PLR_574)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Cholelithiasis and cholecystitis cholelithiasis,
Cholecystitis		 2,059
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001861/ScoringFiles/PGS001861.txt.gz
PGS002072
(portability-ldpred2_574)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Cholelithiasis and cholecystitis cholelithiasis,
Cholecystitis		 428,587
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002072/ScoringFiles/PGS002072.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
PPM001599 PGS000707
(HC225)
 PSS000799|
European Ancestry|
87,413 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Cholecystitis — AUROC: 0.6038 — Age, sex, PCs(1-10) —
PPM007536 PGS000942
(GBE_HC225)
 PSS004364|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cholecystitis — AUROC: 0.68703 [0.64283, 0.73122] R²: 0.05062
Incremental AUROC (full-covars): 0.01542
PGS R2 (no covariates): 0.00638
PGS AUROC (no covariates): 0.57182 [0.52186, 0.62177]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007537 PGS000942
(GBE_HC225)
 PSS004365|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cholecystitis — AUROC: 0.68844 [0.61497, 0.76192] R²: 0.06303
Incremental AUROC (full-covars): 0.01478
PGS R2 (no covariates): 0.00267
PGS AUROC (no covariates): 0.53743 [0.45172, 0.62313]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007538 PGS000942
(GBE_HC225)
 PSS004366|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cholecystitis — AUROC: 0.64946 [0.63161, 0.6673] R²: 0.03849
Incremental AUROC (full-covars): 0.03425
PGS R2 (no covariates): 0.01921
PGS AUROC (no covariates): 0.60901 [0.59053, 0.6275]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007539 PGS000942
(GBE_HC225)
 PSS004367|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cholecystitis — AUROC: 0.65729 [0.62309, 0.69148] R²: 0.04114
Incremental AUROC (full-covars): 0.01289
PGS R2 (no covariates): 0.00646
PGS AUROC (no covariates): 0.56972 [0.5349, 0.60453]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007540 PGS000942
(GBE_HC225)
 PSS004368|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cholecystitis — AUROC: 0.64339 [0.63352, 0.65325] R²: 0.03651
Incremental AUROC (full-covars): 0.03273
PGS R2 (no covariates): 0.01602
PGS AUROC (no covariates): 0.59436 [0.5838, 0.60493]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007541 PGS000943
(GBE_HC1126)
 PSS004144|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholecystitis — AUROC: 0.73752 [0.65767, 0.81736] R²: 0.06767
Incremental AUROC (full-covars): 0.00596
PGS R2 (no covariates): 0.00524
PGS AUROC (no covariates): 0.59329 [0.50586, 0.68073]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007542 PGS000943
(GBE_HC1126)
 PSS004145|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholecystitis — AUROC: 0.8085 [0.69534, 0.92165] R²: 0.14928
Incremental AUROC (full-covars): -0.00085
PGS R2 (no covariates): 0.00478
PGS AUROC (no covariates): 0.41038 [0.27687, 0.54388]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007543 PGS000943
(GBE_HC1126)
 PSS004146|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholecystitis — AUROC: 0.63478 [0.60059, 0.66896] R²: 0.02044
Incremental AUROC (full-covars): 0.00654
PGS R2 (no covariates): 0.00332
PGS AUROC (no covariates): 0.52696 [0.48804, 0.56587]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007544 PGS000943
(GBE_HC1126)
 PSS004147|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholecystitis — AUROC: 0.64056 [0.57812, 0.70301] R²: 0.02887
Incremental AUROC (full-covars): 0.01113
PGS R2 (no covariates): 0.00762
PGS AUROC (no covariates): 0.56004 [0.4865, 0.63358]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007545 PGS000943
(GBE_HC1126)
 PSS004148|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE cholecystitis — AUROC: 0.59655 [0.57661, 0.6165] R²: 0.01081
Incremental AUROC (full-covars): 0.00936
PGS R2 (no covariates): 0.00239
PGS AUROC (no covariates): 0.53954 [0.51772, 0.56136]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009777 PGS001861
(portability-PLR_574)
 PSS009336|
European Ancestry|
19,908 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0948 [0.081, 0.1085] sex, age, birth date, deprivation index, 16 PCs —
PPM009778 PGS001861
(portability-PLR_574)
 PSS009110|
European Ancestry|
4,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0809 [0.0504, 0.1112] sex, age, birth date, deprivation index, 16 PCs —
PPM009779 PGS001861
(portability-PLR_574)
 PSS008664|
European Ancestry|
6,631 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0769 [0.0529, 0.1008] sex, age, birth date, deprivation index, 16 PCs —
PPM009780 PGS001861
(portability-PLR_574)
 PSS008438|
Greater Middle Eastern Ancestry|
1,197 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0684 [0.0113, 0.1251] sex, age, birth date, deprivation index, 16 PCs —
PPM009781 PGS001861
(portability-PLR_574)
 PSS008218|
South Asian Ancestry|
6,310 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0422 [0.0175, 0.0668] sex, age, birth date, deprivation index, 16 PCs —
PPM009782 PGS001861
(portability-PLR_574)
 PSS007999|
East Asian Ancestry|
1,806 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.041 [-0.0054, 0.0872] sex, age, birth date, deprivation index, 16 PCs —
PPM009783 PGS001861
(portability-PLR_574)
 PSS007783|
African Ancestry|
2,477 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0362 [-0.0033, 0.0757] sex, age, birth date, deprivation index, 16 PCs —
PPM009784 PGS001861
(portability-PLR_574)
 PSS008887|
African Ancestry|
3,912 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0251 [-0.0063, 0.0565] sex, age, birth date, deprivation index, 16 PCs —
PPM011437 PGS002072
(portability-ldpred2_574)
 PSS009336|
European Ancestry|
19,908 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.098 [0.0842, 0.1117] sex, age, birth date, deprivation index, 16 PCs —
PPM011439 PGS002072
(portability-ldpred2_574)
 PSS008664|
European Ancestry|
6,631 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0805 [0.0565, 0.1044] sex, age, birth date, deprivation index, 16 PCs —
PPM011440 PGS002072
(portability-ldpred2_574)
 PSS008438|
Greater Middle Eastern Ancestry|
1,197 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0663 [0.0092, 0.123] sex, age, birth date, deprivation index, 16 PCs —
PPM011441 PGS002072
(portability-ldpred2_574)
 PSS008218|
South Asian Ancestry|
6,310 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0503 [0.0256, 0.0749] sex, age, birth date, deprivation index, 16 PCs —
PPM011442 PGS002072
(portability-ldpred2_574)
 PSS007999|
East Asian Ancestry|
1,806 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0441 [-0.0023, 0.0903] sex, age, birth date, deprivation index, 16 PCs —
PPM011443 PGS002072
(portability-ldpred2_574)
 PSS007783|
African Ancestry|
2,477 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0336 [-0.0059, 0.0731] sex, age, birth date, deprivation index, 16 PCs —
PPM011444 PGS002072
(portability-ldpred2_574)
 PSS008887|
African Ancestry|
3,912 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.033 [0.0016, 0.0643] sex, age, birth date, deprivation index, 16 PCs —
PPM011438 PGS002072
(portability-ldpred2_574)
 PSS009110|
European Ancestry|
4,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0792 [0.0487, 0.1096] 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
PSS008664 — — 6,631 individuals — European Italy (South Europe) UKB —
PSS007783 — — 2,477 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008438 — — 1,197 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009336 — — 19,908 individuals — European UK (+ Ireland) UKB —
PSS004364 — —
[
  • 128 cases
  • , 6,369 controls
]
 — African unspecified — UKB —
PSS004365 — —
[
  • 48 cases
  • , 1,656 controls
]
 — East Asian — UKB —
PSS004366 — —
[
  • 926 cases
  • , 23,979 controls
]
 — European non-white British ancestry UKB —
PSS004367 — —
[
  • 256 cases
  • , 7,575 controls
]
 — South Asian — UKB —
PSS004368 — —
[
  • 2,978 cases
  • , 64,447 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS009110 — — 4,121 individuals — European Poland (NE Europe) UKB —
PSS008218 — — 6,310 individuals — South Asian India (South Asia) UKB —
PSS000799 — — 87,413 individuals — European — UKB —
PSS008887 — — 3,912 individuals — African unspecified Nigeria (West Africa) UKB —
PSS004144 — —
[
  • 35 cases
  • , 6,462 controls
]
 — African unspecified — UKB —
PSS004145 — —
[
  • 14 cases
  • , 1,690 controls
]
 — East Asian — UKB —
PSS004146 — —
[
  • 233 cases
  • , 24,672 controls
]
 — European non-white British ancestry UKB —
PSS004147 — —
[
  • 66 cases
  • , 7,765 controls
]
 — South Asian — UKB —
PSS004148 — —
[
  • 706 cases
  • , 66,719 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS007999 — — 1,806 individuals — East Asian China (East Asia) UKB —