Trait: Abdominal pain

Trait Information
Identifier HP_0002027
Description An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) and perceived to originate in the abdomen.
Trait category
Other trait
Synonyms 7 synonyms
  • Abdominal discomfort
  • Abdominal pain
  • Gastro pain
  • Gastrointestinal pain
  • Pain in stomach
  • Stomach pain
  • Upset stomach
Mapped terms 6 mapped terms
  • ICD9:789.0
  • MEDDRA:10000081
  • NCIt:C26682
  • SNOMEDCT:21522001
  • SNOMEDCT_US:21522001
  • UMLS:C0000737

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)
PGS001395
(GBE_INI21025)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Frequency of discomfort/pain in abdomen in last 3 months Abdominal pain 256
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001395/ScoringFiles/PGS001395.txt.gz
PGS001884
(portability-PLR_785)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Abdominal pain Abdominal pain 2,796
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001884/ScoringFiles/PGS001884.txt.gz
PGS002096
(portability-ldpred2_785)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Abdominal pain Abdominal pain 791,954
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002096/ScoringFiles/PGS002096.txt.gz
PGS004497
(disease.R10.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 R10 (Abdominal and pelvic pain) Abdominal pain 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004497/ScoringFiles/PGS004497.txt.gz
PGS004567
(meta.R10.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 R10 (Abdominal and pelvic pain) Abdominal pain 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004567/ScoringFiles/PGS004567.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
PPM005260 PGS001395
(GBE_INI21025)
 PSS004921|
African Ancestry|
1,000 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of discomfort/pain in abdomen in last 3 months — — R²: 0.03492 [0.02615, 0.04369]
Incremental R2 (full-covars): -0.00145
PGS R2 (no covariates): 0.00039 [-0.00057, 0.00135]		 age, sex, UKB array type, Genotype PCs —
PPM005261 PGS001395
(GBE_INI21025)
 PSS004922|
East Asian Ancestry|
393 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of discomfort/pain in abdomen in last 3 months — — R²: 0.05489 [0.03391, 0.07588]
Incremental R2 (full-covars): 0.00278
PGS R2 (no covariates): 0.00489 [-0.0017, 0.01149]		 age, sex, UKB array type, Genotype PCs —
PPM005262 PGS001395
(GBE_INI21025)
 PSS004923|
European Ancestry|
9,133 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of discomfort/pain in abdomen in last 3 months — — R²: 0.02414 [0.02037, 0.02791]
Incremental R2 (full-covars): 0.00038
PGS R2 (no covariates): 0.00058 [-0.00002, 0.00118]		 age, sex, UKB array type, Genotype PCs —
PPM005263 PGS001395
(GBE_INI21025)
 PSS004924|
South Asian Ancestry|
1,189 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of discomfort/pain in abdomen in last 3 months — — R²: 0.04706 [0.03791, 0.05622]
Incremental R2 (full-covars): 0.00161
PGS R2 (no covariates): 0.00255 [0.00032, 0.00477]		 age, sex, UKB array type, Genotype PCs —
PPM005264 PGS001395
(GBE_INI21025)
 PSS004925|
European Ancestry|
24,424 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of discomfort/pain in abdomen in last 3 months — — R²: 0.03134 [0.02875, 0.03392]
Incremental R2 (full-covars): 0.00091
PGS R2 (no covariates): 0.00095 [0.00049, 0.00142]		 age, sex, UKB array type, Genotype PCs —
PPM038871 PGS001395
(GBE_INI21025)
 PSS013916|
European Ancestry|
425,240 individuals
 PGP000865 |
Bhatt IS et al. J Assoc Res Otolaryngol (2024)
|Ext.		 Reported Trait: Age-related hearing difficulty β: 0.01547 — — — —
PPM009957 PGS001884
(portability-PLR_785)
 PSS009135|
European Ancestry|
4,136 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0569 [0.0264, 0.0873] sex, age, birth date, deprivation index, 16 PCs —
PPM009958 PGS001884
(portability-PLR_785)
 PSS008689|
European Ancestry|
6,660 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0156 [-0.0085, 0.0396] sex, age, birth date, deprivation index, 16 PCs —
PPM009956 PGS001884
(portability-PLR_785)
 PSS009361|
European Ancestry|
20,000 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0265 [0.0126, 0.0403] sex, age, birth date, deprivation index, 16 PCs —
PPM009959 PGS001884
(portability-PLR_785)
 PSS008463|
Greater Middle Eastern Ancestry|
1,200 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): -0.0034 [-0.0605, 0.0536] sex, age, birth date, deprivation index, 16 PCs —
PPM009960 PGS001884
(portability-PLR_785)
 PSS008243|
South Asian Ancestry|
6,331 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0214 [-0.0033, 0.046] sex, age, birth date, deprivation index, 16 PCs —
PPM009961 PGS001884
(portability-PLR_785)
 PSS008021|
East Asian Ancestry|
1,810 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0135 [-0.0329, 0.0598] sex, age, birth date, deprivation index, 16 PCs —
PPM009962 PGS001884
(portability-PLR_785)
 PSS007807|
African Ancestry|
2,484 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0188 [-0.0207, 0.0583] sex, age, birth date, deprivation index, 16 PCs —
PPM009963 PGS001884
(portability-PLR_785)
 PSS008911|
African Ancestry|
3,924 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0049 [-0.0265, 0.0362] sex, age, birth date, deprivation index, 16 PCs —
PPM038594 PGS001884
(portability-PLR_785)
 PSS013916|
European Ancestry|
425,240 individuals
 PGP000865 |
Bhatt IS et al. J Assoc Res Otolaryngol (2024)
|Ext.		 Reported Trait: Age-related hearing difficulty β: 0.02589 — — — —
PPM011624 PGS002096
(portability-ldpred2_785)
 PSS009361|
European Ancestry|
20,000 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0549 [0.041, 0.0687] sex, age, birth date, deprivation index, 16 PCs —
PPM011625 PGS002096
(portability-ldpred2_785)
 PSS009135|
European Ancestry|
4,136 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.1007 [0.0704, 0.1309] sex, age, birth date, deprivation index, 16 PCs —
PPM011626 PGS002096
(portability-ldpred2_785)
 PSS008689|
European Ancestry|
6,660 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0453 [0.0212, 0.0693] sex, age, birth date, deprivation index, 16 PCs —
PPM011627 PGS002096
(portability-ldpred2_785)
 PSS008463|
Greater Middle Eastern Ancestry|
1,200 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0212 [-0.0359, 0.0782] sex, age, birth date, deprivation index, 16 PCs —
PPM011628 PGS002096
(portability-ldpred2_785)
 PSS008243|
South Asian Ancestry|
6,331 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0273 [0.0027, 0.052] sex, age, birth date, deprivation index, 16 PCs —
PPM011629 PGS002096
(portability-ldpred2_785)
 PSS008021|
East Asian Ancestry|
1,810 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0088 [-0.0376, 0.0551] sex, age, birth date, deprivation index, 16 PCs —
PPM011630 PGS002096
(portability-ldpred2_785)
 PSS007807|
African Ancestry|
2,484 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0099 [-0.0296, 0.0493] sex, age, birth date, deprivation index, 16 PCs —
PPM011631 PGS002096
(portability-ldpred2_785)
 PSS008911|
African Ancestry|
3,924 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Abdominal pain — — Partial Correlation (partial-r): 0.0476 [0.0163, 0.0789] sex, age, birth date, deprivation index, 16 PCs —
PPM038353 PGS002096
(portability-ldpred2_785)
 PSS013916|
European Ancestry|
425,240 individuals
 PGP000865 |
Bhatt IS et al. J Assoc Res Otolaryngol (2024)
|Ext.		 Reported Trait: Age-related hearing difficulty β: 0.06624 — — — —
PPM020612 PGS004497
(disease.R10.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: R10 (Abdominal and pelvic pain) OR: 1.12745 — — — —
PPM020682 PGS004567
(meta.R10.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: R10 (Abdominal and pelvic pain) OR: 1.17946 — — — —

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
PSS004924 — — 1,189 individuals — South Asian — UKB —
PSS004925 — — 24,424 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS011364 — — 56,192 individuals — European — UKB —
PSS009135 — — 4,136 individuals — European Poland (NE Europe) UKB —
PSS008463 — — 1,200 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008689 — — 6,660 individuals — European Italy (South Europe) UKB —
PSS009361 — — 20,000 individuals — European UK (+ Ireland) UKB —
PSS008243 — — 6,331 individuals — South Asian India (South Asia) UKB —
PSS008911 — — 3,924 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008021 — — 1,810 individuals — East Asian China (East Asia) UKB —
PSS007807 — — 2,484 individuals — African American or Afro-Caribbean Carribean UKB —
PSS013916 — —
[
  • 111,243 cases
  • , 313,997 controls
]
,
46.21 % Male samples
 — European
(British, Irish)		 — UKB —
PSS004921 — — 1,000 individuals — African unspecified — UKB —
PSS004922 — — 393 individuals — East Asian — UKB —
PSS004923 — — 9,133 individuals — European non-white British ancestry UKB —