Trait: small intestine disorder

Trait Information
Identifier MONDO_0024635
Description A disease that involves the small intestine. [MONDO: patterns/location]
Trait categories
Digestive system disorder
Other disease
Synonyms 4 synonyms
  • disease of small intestine
  • disease or disorder of small intestine
  • disorder of small intestine
  • small intestine disease or disorder
Child trait(s) 3 child traits

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
Note: This table shows PGS for child terms of "small intestine disorder" in the EFO hierarchy.
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)
PGS000040
(GRS_CeD)
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Coeliac disease celiac disease 228
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000040/ScoringFiles/PGS000040.txt.gz
PGS000041
(GRS-DQ2.5-CeD)
 PGP000029 |
Abraham G et al. Genome Med (2015)
 Coeliac disease celiac disease 2,513
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000041/ScoringFiles/PGS000041.txt.gz
PGS000042
(GRS-DQ2.5-CeD-imputed)
 PGP000029 |
Abraham G et al. Genome Med (2015)
 Coeliac disease celiac disease 3,317
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000042/ScoringFiles/PGS000042.txt.gz
PGS000316
(GRS42_Coeliac)
 PGP000093 |
Sharp SA et al. Aliment Pharmacol Ther (2020)
 Coeliac disease celiac disease 53
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000316/ScoringFiles/PGS000316.txt.gz
PGS001300
(GBE_BIN21068)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Celiac disease or gluten sensitivity, diagnosed celiac disease 9
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001300/ScoringFiles/PGS001300.txt.gz
PGS001301
(GBE_HC303)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Malabsorption/coeliac disease celiac disease 428
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001301/ScoringFiles/PGS001301.txt.gz
PGS001390
(GBE_HC1084)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Duodenal ulcer (time-to-event) duodenal ulcer 220
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001390/ScoringFiles/PGS001390.txt.gz
PGS001852
(portability-PLR_535.6)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Duodenitis duodenitis 191
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001852/ScoringFiles/PGS001852.txt.gz
PGS001856
(portability-PLR_557.1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Celiac disease celiac disease 1,661
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001856/ScoringFiles/PGS001856.txt.gz
PGS001894
(portability-PLR_celiac_gluten)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Diagnosed with coeliac disease or gluten sensitivity celiac disease 484
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001894/ScoringFiles/PGS001894.txt.gz
PGS002067
(portability-ldpred2_557.1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Celiac disease celiac disease 58,231
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002067/ScoringFiles/PGS002067.txt.gz
PGS002107
(portability-ldpred2_celiac_gluten)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Diagnosed with coeliac disease or gluten sensitivity celiac disease 39,066
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002107/ScoringFiles/PGS002107.txt.gz
PGS004930
(celiac_disease_snpnet_combined)
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Celiac disease celiac disease 463
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004930/ScoringFiles/PGS004930.txt.gz
PGS019335
(TPMI_531.3_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Duodenal ulcer duodenal ulcer 19
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019335/ScoringFiles/PGS019335.txt.gz
PGS019336
(TPMI_531.3_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Duodenal ulcer duodenal ulcer 939,880
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019336/ScoringFiles/PGS019336.txt.gz
PGS019337
(TPMI_531.3_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Duodenal ulcer duodenal ulcer 21,469
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019337/ScoringFiles/PGS019337.txt.gz
PGS019338
(TPMI_531.3_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Duodenal ulcer duodenal ulcer 983,821
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019338/ScoringFiles/PGS019338.txt.gz
PGS019339
(TPMI_531.3_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Duodenal ulcer duodenal ulcer 966,134
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019339/ScoringFiles/PGS019339.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
PPM000093 PGS000040
(GRS_CeD)
 PSS000059|
European Ancestry|
2,476 individuals
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Reported Trait: Coeliac disease — AUROC: 0.9 — — —
PPM000094 PGS000040
(GRS_CeD)
 PSS000061|
European Ancestry|
1,040 individuals
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Reported Trait: Coeliac disease — AUROC: 0.87 — — —
PPM000095 PGS000040
(GRS_CeD)
 PSS000062|
European Ancestry|
1,649 individuals
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Reported Trait: Coeliac disease — AUROC: 0.86 — — —
PPM000096 PGS000040
(GRS_CeD)
 PSS000063|
European Ancestry|
2,200 individuals
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Reported Trait: Coeliac disease — AUROC: 0.87 — — —
PPM000097 PGS000040
(GRS_CeD)
 PSS000060|
European Ancestry|
10,304 individuals
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Reported Trait: Coeliac disease — AUROC: 0.87 — — —
PPM000098 PGS000040
(GRS_CeD)
 PSS000064|
European Ancestry|
1,696 individuals
 PGP000029 |
Abraham G et al. Genome Med (2015)
|Ext.		 Reported Trait: Coeliac disease — AUROC: 0.831 [0.808, 0.85] — — —
PPM000099 PGS000040
(GRS_CeD)
 PSS000065|
European Ancestry|
1,237 individuals
 PGP000029 |
Abraham G et al. Genome Med (2015)
|Ext.		 Reported Trait: Coeliac disease in HLA-DQ2.5 carriers — AUROC: 0.669 [0.625, 0.713] — — —
PPM000100 PGS000041
(GRS-DQ2.5-CeD)
 PSS000065|
European Ancestry|
1,237 individuals
 PGP000029 |
Abraham G et al. Genome Med (2015)
 Reported Trait: Coeliac disease in HLA-DQ2.5 carriers — AUROC: 0.718 [0.676, 0.761] — — —
PPM000101 PGS000042
(GRS-DQ2.5-CeD-imputed)
 PSS000065|
European Ancestry|
1,237 individuals
 PGP000029 |
Abraham G et al. Genome Med (2015)
 Reported Trait: Coeliac disease in HLA-DQ2.5 carriers — AUROC: 0.73 [0.687, 0.772] — — —
PPM000805 PGS000316
(GRS42_Coeliac)
 PSS000381|
Ancestry Not Reported|
154 individuals
 PGP000093 |
Sharp SA et al. Aliment Pharmacol Ther (2020)
 Reported Trait: Coeliac disease — AUROC: 0.835 [0.76, 0.911] — — —
PPM000804 PGS000316
(GRS42_Coeliac)
 PSS000382|
European Ancestry|
379,767 individuals
 PGP000093 |
Sharp SA et al. Aliment Pharmacol Ther (2020)
 Reported Trait: Coeliac disease — AUROC: 0.879 [0.87, 0.888] — — —
PPM008997 PGS001300
(GBE_BIN21068)
 PSS003667|
African Ancestry|
969 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — AUROC: 0.77521 [0.67165, 0.87877] R²: 0.10494
Incremental AUROC (full-covars): 0.00391
PGS R2 (no covariates): 0.00465
PGS AUROC (no covariates): 0.54048 [0.39518, 0.68579]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008998 PGS001300
(GBE_BIN21068)
 PSS003668|
European Ancestry|
9,024 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — AUROC: 0.67118 [0.63561, 0.70676] R²: 0.04801
Incremental AUROC (full-covars): 0.03638
PGS R2 (no covariates): 0.02217
PGS AUROC (no covariates): 0.58541 [0.54195, 0.62888]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008999 PGS001300
(GBE_BIN21068)
 PSS003669|
South Asian Ancestry|
1,145 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — AUROC: 0.78803 [0.69728, 0.87878] R²: 0.09336
Incremental AUROC (full-covars): 0.00365
PGS R2 (no covariates): 0.00127
PGS AUROC (no covariates): 0.56184 [0.43287, 0.6908]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009000 PGS001300
(GBE_BIN21068)
 PSS003670|
European Ancestry|
24,310 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — AUROC: 0.6734 [0.64935, 0.69745] R²: 0.04185
Incremental AUROC (full-covars): 0.08398
PGS R2 (no covariates): 0.02957
PGS AUROC (no covariates): 0.62888 [0.60094, 0.65683]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009001 PGS001301
(GBE_HC303)
 PSS004423|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malabsorption/coeliac disease — AUROC: 0.84259 [0.73437, 0.95081] R²: 0.12308
Incremental AUROC (full-covars): 0.02463
PGS R2 (no covariates): 0.03018
PGS AUROC (no covariates): 0.68151 [0.48835, 0.87467]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009002 PGS001301
(GBE_HC303)
 PSS004424|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malabsorption/coeliac disease — AUROC: 0.81472 [0.7798, 0.84965] R²: 0.15108
Incremental AUROC (full-covars): 0.1791
PGS R2 (no covariates): 0.14221
PGS AUROC (no covariates): 0.80994 [0.77441, 0.84547]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009003 PGS001301
(GBE_HC303)
 PSS004425|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malabsorption/coeliac disease — AUROC: 0.81699 [0.73267, 0.9013] R²: 0.11397
Incremental AUROC (full-covars): 0.06035
PGS R2 (no covariates): 0.07098
PGS AUROC (no covariates): 0.76239 [0.65258, 0.87221]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009004 PGS001301
(GBE_HC303)
 PSS004426|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malabsorption/coeliac disease — AUROC: 0.83351 [0.81372, 0.85329] R²: 0.14905
Incremental AUROC (full-covars): 0.25775
PGS R2 (no covariates): 0.14224
PGS AUROC (no covariates): 0.82867 [0.80826, 0.84908]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005200 PGS001390
(GBE_HC1084)
 PSS004094|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.71018 [0.66062, 0.75975] R²: 0.05605
Incremental AUROC (full-covars): 0.00294
PGS R2 (no covariates): 0.00399
PGS AUROC (no covariates): 0.5623 [0.50635, 0.61825]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005201 PGS001390
(GBE_HC1084)
 PSS004095|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.66565 [0.55325, 0.77805] R²: 0.04606
Incremental AUROC (full-covars): 0.00253
PGS R2 (no covariates): 0.006
PGS AUROC (no covariates): 0.56376 [0.43513, 0.6924]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005202 PGS001390
(GBE_HC1084)
 PSS004096|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.71045 [0.68829, 0.73261] R²: 0.06289
Incremental AUROC (full-covars): 0.0043
PGS R2 (no covariates): 0.0047
PGS AUROC (no covariates): 0.55991 [0.53425, 0.58556]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005203 PGS001390
(GBE_HC1084)
 PSS004097|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.70619 [0.66443, 0.74795] R²: 0.0567
Incremental AUROC (full-covars): 0.00581
PGS R2 (no covariates): 0.00168
PGS AUROC (no covariates): 0.54031 [0.491, 0.58961]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005204 PGS001390
(GBE_HC1084)
 PSS004098|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE duodenal ulcer — AUROC: 0.68746 [0.67261, 0.70231] R²: 0.04811
Incremental AUROC (full-covars): 0.00644
PGS R2 (no covariates): 0.00484
PGS AUROC (no covariates): 0.56101 [0.54453, 0.5775]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009706 PGS001852
(portability-PLR_535.6)
 PSS009327|
European Ancestry|
18,600 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.0198 [0.0055, 0.0342] sex, age, birth date, deprivation index, 16 PCs —
PPM009707 PGS001852
(portability-PLR_535.6)
 PSS009101|
European Ancestry|
3,868 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.0235 [-0.0081, 0.0551] sex, age, birth date, deprivation index, 16 PCs —
PPM009708 PGS001852
(portability-PLR_535.6)
 PSS008655|
European Ancestry|
6,233 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): -0.0217 [-0.0465, 0.0032] sex, age, birth date, deprivation index, 16 PCs —
PPM009709 PGS001852
(portability-PLR_535.6)
 PSS008429|
Greater Middle Eastern Ancestry|
1,076 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.002 [-0.0583, 0.0623] sex, age, birth date, deprivation index, 16 PCs —
PPM009710 PGS001852
(portability-PLR_535.6)
 PSS008209|
South Asian Ancestry|
5,720 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.0315 [0.0055, 0.0574] sex, age, birth date, deprivation index, 16 PCs —
PPM009711 PGS001852
(portability-PLR_535.6)
 PSS007991|
East Asian Ancestry|
1,684 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.0278 [-0.0203, 0.0757] sex, age, birth date, deprivation index, 16 PCs —
PPM009712 PGS001852
(portability-PLR_535.6)
 PSS007774|
African Ancestry|
2,298 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): -0.0208 [-0.0618, 0.0203] sex, age, birth date, deprivation index, 16 PCs —
PPM009713 PGS001852
(portability-PLR_535.6)
 PSS008878|
African Ancestry|
3,648 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.0077 [-0.0249, 0.0402] sex, age, birth date, deprivation index, 16 PCs —
PPM009738 PGS001856
(portability-PLR_557.1)
 PSS009331|
European Ancestry|
16,106 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.1196 [0.1043, 0.1348] sex, age, birth date, deprivation index, 16 PCs —
PPM009739 PGS001856
(portability-PLR_557.1)
 PSS009105|
European Ancestry|
3,509 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0779 [0.0448, 0.1108] sex, age, birth date, deprivation index, 16 PCs —
PPM009740 PGS001856
(portability-PLR_557.1)
 PSS008659|
European Ancestry|
5,445 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.097 [0.0706, 0.1233] sex, age, birth date, deprivation index, 16 PCs —
PPM009741 PGS001856
(portability-PLR_557.1)
 PSS008433|
Greater Middle Eastern Ancestry|
998 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0652 [0.0025, 0.1273] sex, age, birth date, deprivation index, 16 PCs —
PPM009742 PGS001856
(portability-PLR_557.1)
 PSS008213|
South Asian Ancestry|
5,277 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0535 [0.0265, 0.0805] sex, age, birth date, deprivation index, 16 PCs —
PPM009743 PGS001856
(portability-PLR_557.1)
 PSS007778|
African Ancestry|
2,091 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0261 [-0.017, 0.0691] sex, age, birth date, deprivation index, 16 PCs —
PPM009744 PGS001856
(portability-PLR_557.1)
 PSS008882|
African Ancestry|
3,455 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.028 [-0.0054, 0.0614] sex, age, birth date, deprivation index, 16 PCs —
PPM010037 PGS001894
(portability-PLR_celiac_gluten)
 PSS009164|
European Ancestry|
1,354 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0796 [0.026, 0.1327] sex, age, birth date, deprivation index, 16 PCs —
PPM010038 PGS001894
(portability-PLR_celiac_gluten)
 PSS008718|
European Ancestry|
2,442 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0358 [-0.0041, 0.0755] sex, age, birth date, deprivation index, 16 PCs —
PPM010039 PGS001894
(portability-PLR_celiac_gluten)
 PSS008492|
Greater Middle Eastern Ancestry|
208 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0295 [-0.1141, 0.1719] sex, age, birth date, deprivation index, 16 PCs —
PPM010040 PGS001894
(portability-PLR_celiac_gluten)
 PSS008270|
South Asian Ancestry|
908 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0219 [-0.0439, 0.0876] sex, age, birth date, deprivation index, 16 PCs —
PPM010041 PGS001894
(portability-PLR_celiac_gluten)
 PSS007834|
African Ancestry|
400 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): -0.0127 [-0.1132, 0.088] sex, age, birth date, deprivation index, 16 PCs —
PPM010042 PGS001894
(portability-PLR_celiac_gluten)
 PSS008938|
African Ancestry|
526 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0162 [-0.0711, 0.1032] sex, age, birth date, deprivation index, 16 PCs —
PPM010036 PGS001894
(portability-PLR_celiac_gluten)
 PSS009390|
European Ancestry|
7,142 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0993 [0.0763, 0.1223] sex, age, birth date, deprivation index, 16 PCs —
PPM011398 PGS002067
(portability-ldpred2_557.1)
 PSS009331|
European Ancestry|
16,106 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.1241 [0.1088, 0.1393] sex, age, birth date, deprivation index, 16 PCs —
PPM011400 PGS002067
(portability-ldpred2_557.1)
 PSS008659|
European Ancestry|
5,445 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0979 [0.0714, 0.1242] sex, age, birth date, deprivation index, 16 PCs —
PPM011401 PGS002067
(portability-ldpred2_557.1)
 PSS008433|
Greater Middle Eastern Ancestry|
998 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0718 [0.0092, 0.1339] sex, age, birth date, deprivation index, 16 PCs —
PPM011402 PGS002067
(portability-ldpred2_557.1)
 PSS008213|
South Asian Ancestry|
5,277 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0512 [0.0242, 0.0781] sex, age, birth date, deprivation index, 16 PCs —
PPM011403 PGS002067
(portability-ldpred2_557.1)
 PSS007778|
African Ancestry|
2,091 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0094 [-0.0337, 0.0525] sex, age, birth date, deprivation index, 16 PCs —
PPM011404 PGS002067
(portability-ldpred2_557.1)
 PSS008882|
African Ancestry|
3,455 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0241 [-0.0093, 0.0575] sex, age, birth date, deprivation index, 16 PCs —
PPM011399 PGS002067
(portability-ldpred2_557.1)
 PSS009105|
European Ancestry|
3,509 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0695 [0.0364, 0.1024] sex, age, birth date, deprivation index, 16 PCs —
PPM011712 PGS002107
(portability-ldpred2_celiac_gluten)
 PSS009390|
European Ancestry|
7,142 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0964 [0.0733, 0.1193] sex, age, birth date, deprivation index, 16 PCs —
PPM011713 PGS002107
(portability-ldpred2_celiac_gluten)
 PSS009164|
European Ancestry|
1,354 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0848 [0.0313, 0.1379] sex, age, birth date, deprivation index, 16 PCs —
PPM011714 PGS002107
(portability-ldpred2_celiac_gluten)
 PSS008718|
European Ancestry|
2,442 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.041 [0.0012, 0.0807] sex, age, birth date, deprivation index, 16 PCs —
PPM011715 PGS002107
(portability-ldpred2_celiac_gluten)
 PSS008492|
Greater Middle Eastern Ancestry|
208 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0206 [-0.1229, 0.1632] sex, age, birth date, deprivation index, 16 PCs —
PPM011716 PGS002107
(portability-ldpred2_celiac_gluten)
 PSS008270|
South Asian Ancestry|
908 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0237 [-0.0422, 0.0893] sex, age, birth date, deprivation index, 16 PCs —
PPM011717 PGS002107
(portability-ldpred2_celiac_gluten)
 PSS007834|
African Ancestry|
400 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): -0.0242 [-0.1245, 0.0766] sex, age, birth date, deprivation index, 16 PCs —
PPM011718 PGS002107
(portability-ldpred2_celiac_gluten)
 PSS008938|
African Ancestry|
526 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0172 [-0.0701, 0.1042] sex, age, birth date, deprivation index, 16 PCs —
PPM021718 PGS004930
(celiac_disease_snpnet_combined)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: Celiac disease OR: 1.52 [1.35, 1.71] AUROC: 0.67 — — —
PPM037517 PGS019335
(TPMI_531.3_Lassosum2)
 PSS013233|
East Asian Ancestry|
16,641 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Duodenal ulcer — AUROC: 0.63988 R²: 0.0376 sex, age, array, PCs 1-10 —
PPM037518 PGS019336
(TPMI_531.3_LDpred2)
 PSS013232|
East Asian Ancestry|
16,641 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Duodenal ulcer — AUROC: 0.64014 R²: 0.03815 sex, age, array, PCs 1-10 —
PPM037519 PGS019337
(TPMI_531.3_MegaPRS)
 PSS013234|
East Asian Ancestry|
16,641 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Duodenal ulcer — AUROC: 0.63826 R²: 0.03705 sex, age, array, PCs 1-10 —
PPM037520 PGS019338
(TPMI_531.3_PRS-CS)
 PSS013235|
East Asian Ancestry|
16,641 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Duodenal ulcer — AUROC: 0.6384 R²: 0.03702 sex, age, array, PCs 1-10 —
PPM037521 PGS019339
(TPMI_531.3_SBayesR)
 PSS013236|
East Asian Ancestry|
16,641 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Duodenal ulcer — AUROC: 0.63913 R²: 0.03711 sex, age, array, PCs 1-10 —

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
PSS009164 — — 1,354 individuals — European Poland (NE Europe) UKB —
PSS008270 — — 908 individuals — South Asian India (South Asia) UKB —
PSS004423 — —
[
  • 7 cases
  • , 6,490 controls
]
 — African unspecified — UKB —
PSS004424 — —
[
  • 178 cases
  • , 24,727 controls
]
 — European non-white British ancestry UKB —
PSS004425 — —
[
  • 24 cases
  • , 7,807 controls
]
 — South Asian — UKB —
PSS004426 — —
[
  • 451 cases
  • , 66,974 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS008655 — — 6,233 individuals — European Italy (South Europe) UKB —
PSS008659 — — 5,445 individuals — European Italy (South Europe) UKB —
PSS003667 — —
[
  • 18 cases
  • , 951 controls
]
 — African unspecified — UKB —
PSS003668 — —
[
  • 213 cases
  • , 8,811 controls
]
 — European non-white British ancestry UKB —
PSS003669 — —
[
  • 16 cases
  • , 1,129 controls
]
 — South Asian — UKB —
PSS003670 — —
[
  • 468 cases
  • , 23,842 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS007774 — — 2,298 individuals — African American or Afro-Caribbean Carribean UKB —
PSS007778 — — 2,091 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008938 — — 526 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008429 — — 1,076 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009327 — — 18,600 individuals — European UK (+ Ireland) UKB —
PSS008433 — — 998 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009331 — — 16,106 individuals — European UK (+ Ireland) UKB —
PSS013232 532.1, 532.3, 532.5, 532.7, 532.9,K26 —
[
  • 643 cases
  • , 15,998 controls
]
,
46.01 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013233 532.1, 532.3, 532.5, 532.7, 532.9,K26 —
[
  • 643 cases
  • , 15,998 controls
]
,
46.01 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013234 532.1, 532.3, 532.5, 532.7, 532.9,K26 —
[
  • 643 cases
  • , 15,998 controls
]
,
46.01 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013235 532.1, 532.3, 532.5, 532.7, 532.9,K26 —
[
  • 643 cases
  • , 15,998 controls
]
,
46.01 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013236 532.1, 532.3, 532.5, 532.7, 532.9,K26 —
[
  • 643 cases
  • , 15,998 controls
]
,
46.01 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS000381 Control subjects (n = 40) were paediatric general gastroenterology patients whom were negative for coeliac disease by both intestinal biopsy and negative tissue transglutaminase serology. —
[
  • 0 cases
  • , 40 controls
]
,
48.0 % Male samples
 Mean = 4.9 years
Sd = 4.0 years		 NR — STOLLERY_CC —
PSS000381 Diagnosis of coeliac disease was made by a modification of European serological diagnostic guidelines for patients referred to a tertiary paediatric clinic in Alberta, Canada, for consideration of coeliac disease diagnosis —
[
  • 63 cases
  • , 0 controls
]
,
63.0 % Male samples
 Mean = 8.6 years
Sd = 3.9 years		 NR — STOLLERY_CC —
PSS000381 Diagnosis of coeliac disease was made by endoscopy for patients referred to a tertiary paediatric clinic in Alberta, Canada, for consideration of coeliac disease diagnosis —
[
  • 51 cases
  • , 0 controls
]
,
57.0 % Male samples
 Mean = 7.5 years
Sd = 3.8 years		 NR — STOLLERY_CC —
PSS000382 Coeliac disease cases were identified using either hospital admission code and/or self‐reported coeliac disease. —
[
  • 1,237 cases
  • , 378,530 controls
]
 — European — UKB —
PSS004094 — —
[
  • 95 cases
  • , 6,402 controls
]
 — African unspecified — UKB —
PSS004095 — —
[
  • 24 cases
  • , 1,680 controls
]
 — East Asian — UKB —
PSS004096 — —
[
  • 481 cases
  • , 24,424 controls
]
 — European non-white British ancestry UKB —
PSS004097 — —
[
  • 135 cases
  • , 7,696 controls
]
 — South Asian — UKB —
PSS004098 — —
[
  • 1,164 cases
  • , 66,261 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS009101 — — 3,868 individuals — European Poland (NE Europe) UKB —
PSS008718 — — 2,442 individuals — European Italy (South Europe) UKB —
PSS008209 — — 5,720 individuals — South Asian India (South Asia) UKB —
PSS009105 — — 3,509 individuals — European Poland (NE Europe) UKB —
PSS008213 — — 5,277 individuals — South Asian India (South Asia) UKB —
PSS000059 — —
[
  • 647 cases
  • , 1,829 controls
]
 — European
(Finnish)		 — FINRISK, Health2000 —
PSS000060 — —
[
  • 5,907 cases
  • , 4,397 controls
]
 — European
(British)		 — NR Immunochip
PSS000061 — —
[
  • 497 cases
  • , 543 controls
]
 — European
(Italian)		 — NR —
PSS000062 — —
[
  • 803 cases
  • , 846 controls
]
 — European
(Dutch)		 — NR —
PSS000063 — —
[
  • 778 cases
  • , 1,422 controls
]
 — European
(British)		 — NR —
PSS007834 — — 400 individuals — African American or Afro-Caribbean Carribean UKB —
PSS011762 — — 8,417 individuals — European — BBofA —
PSS000064 — —
[
  • 1,259 cases
  • , 437 controls
]
 — European — NIDDK —
PSS000065 The HLA-DQ2.5-positive subset of NIDDK-CIDR —
[
  • 1,094 cases
  • , 143 controls
]
 — European — NIDDK HLA alleles were imputed using SNP2HLA
PSS008492 — — 208 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008878 — — 3,648 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009390 — — 7,142 individuals — European UK (+ Ireland) UKB —
PSS008882 — — 3,455 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007991 — — 1,684 individuals — East Asian China (East Asia) UKB —