Trait: ulcerative colitis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000729
Description An inflammatory bowel disease involving the mucosal surface of the large intestine and rectum. It may present with an acute or slow onset and follows an intermittent or continuous course. Signs and symptoms include abdominal pain, diarrhea, fever, weight loss, and intestinal hemorrhage. [NCIT: P378]
Trait categories
Digestive system disorder
Immune system disorder
Synonyms 15 synonyms
  • Colitis, Ulcerative
  • Left-sided ulcerative (chronic) colitis
  • Left-sided ulcerative colitis
  • Other ulcerative colitis
  • Other ulcerative colitis (disorder)
  • UC
  • UC - ulcerative colitis
  • ULCERATVE COLITIS UNSPCF
  • Ulcerative colitis, unspecified
  • colitis ulcerative
  • left-sided ulcerative colitis
  • ulcerative colitis
  • ulcerative colitis (disease)
  • ulcerative colitis (disorder)
  • ulcerative proctosigmoiditis
Mapped terms 23 mapped terms
  • DOID:8577
  • HP:0100279
  • ICD10:K51
  • ICD9:556
  • ICD9:556.5
  • ICD9:556.8
  • ICD9:556.9
  • MEDGEN:3532
  • MESH:D003093
  • MONDO:0005101
  • MeSH:D003093
  • MedDRA:10045365
  • MedDRA:10045366
  • NANDO:1200449
  • NANDO:2200920
  • NCIT:C2952
  • NCIt:C2952
  • OMIM:266600
  • Orphanet:771
  • SCTID:64766004
  • SNOMEDCT:64766004
  • UMLS:C0009324
  • icd11.foundation:784669405

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)
PGS001306
(GBE_HC201)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Ulcerative colitis ulcerative colitis 179
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001306/ScoringFiles/PGS001306.txt.gz
PGS001307
(GBE_HC1102)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Ulcerative colitis (time-to-event) ulcerative colitis 809
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001307/ScoringFiles/PGS001307.txt.gz
PGS001855
(portability-PLR_555.2)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Ulcerative colitis ulcerative colitis 1,505
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001855/ScoringFiles/PGS001855.txt.gz
PGS002066
(portability-ldpred2_555.2)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Ulcerative colitis ulcerative colitis 566,637
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002066/ScoringFiles/PGS002066.txt.gz
PGS004253
(uc_ldpred2)
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Ulcerative colitis ulcerative colitis 744,575
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004253/ScoringFiles/PGS004253.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
PPM009024 PGS001306
(GBE_HC201)
 PSS004339|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ulcerative colitis — AUROC: 0.62904 [0.5093, 0.74878] R²: 0.04535
Incremental AUROC (full-covars): -0.00864
PGS R2 (no covariates): 0.00044
PGS AUROC (no covariates): 0.51081 [0.37987, 0.64174]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009025 PGS001306
(GBE_HC201)
 PSS004340|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ulcerative colitis — AUROC: 0.89429 [0.79357, 0.99502] R²: 0.20499
Incremental AUROC (full-covars): -0.0033
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.49111 [0.35854, 0.62368]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009026 PGS001306
(GBE_HC201)
 PSS004341|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ulcerative colitis — AUROC: 0.66162 [0.6277, 0.69554] R²: 0.03336
Incremental AUROC (full-covars): 0.04247
PGS R2 (no covariates): 0.02036
PGS AUROC (no covariates): 0.63006 [0.5958, 0.66432]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009027 PGS001306
(GBE_HC201)
 PSS004342|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ulcerative colitis — AUROC: 0.67522 [0.62537, 0.72506] R²: 0.03696
Incremental AUROC (full-covars): 0.01011
PGS R2 (no covariates): 0.00545
PGS AUROC (no covariates): 0.56552 [0.50815, 0.62289]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009028 PGS001306
(GBE_HC201)
 PSS004343|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ulcerative colitis — AUROC: 0.6157 [0.59481, 0.63659] PGS R2 (no covariates): 0.0193
R²: 0.01676
Incremental AUROC (full-covars): 0.08728
PGS AUROC (no covariates): 0.62452 [0.60374, 0.6453]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009029 PGS001307
(GBE_HC1102)
 PSS004119|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE ulcerative colitis — AUROC: 0.62873 [0.51002, 0.74744] R²: 0.04344
Incremental AUROC (full-covars): -0.00895
PGS R2 (no covariates): 0.00027
PGS AUROC (no covariates): 0.50641 [0.39121, 0.62161]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009030 PGS001307
(GBE_HC1102)
 PSS004120|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE ulcerative colitis — AUROC: 0.89582 [0.79576, 0.99588] R²: 0.20607
Incremental AUROC (full-covars): -0.00177
PGS R2 (no covariates): 0.00203
PGS AUROC (no covariates): 0.55433 [0.4473, 0.66136]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009031 PGS001307
(GBE_HC1102)
 PSS004121|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE ulcerative colitis — AUROC: 0.65578 [0.62353, 0.68804] R²: 0.03272
Incremental AUROC (full-covars): 0.04212
PGS R2 (no covariates): 0.0169
PGS AUROC (no covariates): 0.6106 [0.57717, 0.64402]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009032 PGS001307
(GBE_HC1102)
 PSS004122|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE ulcerative colitis — AUROC: 0.66008 [0.61042, 0.70974] R²: 0.03192
Incremental AUROC (full-covars): 0.00203
PGS R2 (no covariates): 0.0036
PGS AUROC (no covariates): 0.55808 [0.506, 0.61016]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009033 PGS001307
(GBE_HC1102)
 PSS004123|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE ulcerative colitis — AUROC: 0.63965 [0.62036, 0.65895] R²: 0.02376
Incremental AUROC (full-covars): 0.1085
PGS R2 (no covariates): 0.02383
PGS AUROC (no covariates): 0.63847 [0.61861, 0.65833]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009730 PGS001855
(portability-PLR_555.2)
 PSS009330|
European Ancestry|
16,188 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0625 [0.0471, 0.0778] sex, age, birth date, deprivation index, 16 PCs —
PPM009732 PGS001855
(portability-PLR_555.2)
 PSS008658|
European Ancestry|
5,477 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0453 [0.0188, 0.0717] sex, age, birth date, deprivation index, 16 PCs —
PPM009733 PGS001855
(portability-PLR_555.2)
 PSS008432|
Greater Middle Eastern Ancestry|
1,007 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0175 [-0.0449, 0.0799] sex, age, birth date, deprivation index, 16 PCs —
PPM009734 PGS001855
(portability-PLR_555.2)
 PSS008212|
South Asian Ancestry|
5,337 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0407 [0.0139, 0.0676] sex, age, birth date, deprivation index, 16 PCs —
PPM009735 PGS001855
(portability-PLR_555.2)
 PSS007994|
East Asian Ancestry|
1,630 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0382 [-0.0107, 0.0868] sex, age, birth date, deprivation index, 16 PCs —
PPM009736 PGS001855
(portability-PLR_555.2)
 PSS007777|
African Ancestry|
2,105 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.031 [-0.0119, 0.0738] sex, age, birth date, deprivation index, 16 PCs —
PPM009737 PGS001855
(portability-PLR_555.2)
 PSS008881|
African Ancestry|
3,465 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): -0.0003 [-0.0337, 0.0331] sex, age, birth date, deprivation index, 16 PCs —
PPM009731 PGS001855
(portability-PLR_555.2)
 PSS009104|
European Ancestry|
3,520 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0367 [0.0036, 0.0698] sex, age, birth date, deprivation index, 16 PCs —
PPM011390 PGS002066
(portability-ldpred2_555.2)
 PSS009330|
European Ancestry|
16,188 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0641 [0.0487, 0.0794] sex, age, birth date, deprivation index, 16 PCs —
PPM011391 PGS002066
(portability-ldpred2_555.2)
 PSS009104|
European Ancestry|
3,520 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0466 [0.0135, 0.0796] sex, age, birth date, deprivation index, 16 PCs —
PPM011392 PGS002066
(portability-ldpred2_555.2)
 PSS008658|
European Ancestry|
5,477 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0426 [0.0161, 0.0691] sex, age, birth date, deprivation index, 16 PCs —
PPM011393 PGS002066
(portability-ldpred2_555.2)
 PSS008432|
Greater Middle Eastern Ancestry|
1,007 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0056 [-0.0568, 0.068] sex, age, birth date, deprivation index, 16 PCs —
PPM011395 PGS002066
(portability-ldpred2_555.2)
 PSS007994|
East Asian Ancestry|
1,630 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0398 [-0.009, 0.0885] sex, age, birth date, deprivation index, 16 PCs —
PPM011396 PGS002066
(portability-ldpred2_555.2)
 PSS007777|
African Ancestry|
2,105 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0272 [-0.0157, 0.0701] sex, age, birth date, deprivation index, 16 PCs —
PPM011397 PGS002066
(portability-ldpred2_555.2)
 PSS008881|
African Ancestry|
3,465 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0058 [-0.0276, 0.0392] sex, age, birth date, deprivation index, 16 PCs —
PPM011394 PGS002066
(portability-ldpred2_555.2)
 PSS008212|
South Asian Ancestry|
5,337 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0388 [0.0119, 0.0656] sex, age, birth date, deprivation index, 16 PCs —
PPM021728 PGS002066
(portability-ldpred2_555.2)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
|Ext.		 Reported Trait: Ulcerative colitis OR: 1.11 [0.97, 1.28] AUROC: 0.57 — — —
PPM020320 PGS004253
(uc_ldpred2)
 PSS011334|
European Ancestry|
21,335 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Ulcerative colitis OR: 1.75 [1.59, 1.92] AUROC: 0.65 [0.62, 0.68] — age, sex, 10 PCs —
PPM020319 PGS004253
(uc_ldpred2)
 PSS011335|
European Ancestry|
5,735 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Ulcerative colitis OR: 1.84 [1.76, 1.93] AUROC: 0.66 [0.64, 0.68] — age at diagnosis/enrollment, sex, genotyping array, 10 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
PSS008658 — — 5,477 individuals — European Italy (South Europe) UKB —
PSS011334 — —
[
  • 459 cases
  • , 20,876 controls
]
 — European — BioVU —
PSS007777 — — 2,105 individuals — African American or Afro-Caribbean Carribean UKB —
PSS011335 — —
[
  • 844 cases
  • , 4,891 controls
]
 — European — UKB —
PSS008432 — — 1,007 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009330 — — 16,188 individuals — European UK (+ Ireland) UKB —
PSS004339 — —
[
  • 27 cases
  • , 6,470 controls
]
 — African unspecified — UKB —
PSS004340 — —
[
  • 5 cases
  • , 1,699 controls
]
 — East Asian — UKB —
PSS004341 — —
[
  • 239 cases
  • , 24,666 controls
]
 — European non-white British ancestry UKB —
PSS004342 — —
[
  • 103 cases
  • , 7,728 controls
]
 — South Asian — UKB —
PSS004343 — —
[
  • 720 cases
  • , 66,705 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS009104 — — 3,520 individuals — European Poland (NE Europe) UKB —
PSS008212 — — 5,337 individuals — South Asian India (South Asia) UKB —
PSS011762 — — 8,417 individuals — European — BBofA —
PSS004119 — —
[
  • 27 cases
  • , 6,470 controls
]
 — African unspecified — UKB —
PSS004120 — —
[
  • 5 cases
  • , 1,699 controls
]
 — East Asian — UKB —
PSS004121 — —
[
  • 260 cases
  • , 24,645 controls
]
 — European non-white British ancestry UKB —
PSS004122 — —
[
  • 113 cases
  • , 7,718 controls
]
 — South Asian — UKB —
PSS004123 — —
[
  • 788 cases
  • , 66,637 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS008881 — — 3,465 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007994 — — 1,630 individuals — East Asian China (East Asia) UKB —