Trait: hypnic headache

Trait Information
Identifier MONDO_0017181
Description Conditions in which the primary symptom is headache and the headache cannot be attributed to any known causes. [MESH: D051270]
Trait category
Other trait
Synonyms 2 synonyms
  • hypnic headache
  • hypnic headache (disease)
Child trait(s) migraine disorder

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 "hypnic headache" 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)
PGS001281
(GBE_HC86)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Migraine migraine disorder 25
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001281/ScoringFiles/PGS001281.txt.gz
PGS001282
(GBE_HC815)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Migraine (time-to-event) migraine disorder 329
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001282/ScoringFiles/PGS001282.txt.gz
PGS004797
(migraine_PRSmix_eur)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Migraine migraine disorder 23
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004797/ScoringFiles/PGS004797.txt.gz
PGS004798
(migraine_PRSmix_sas)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Migraine migraine disorder 3,984,158
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004798/ScoringFiles/PGS004798.txt.gz
PGS004799
(migraine_PRSmixPlus_eur)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Migraine migraine disorder 4,319,950
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004799/ScoringFiles/PGS004799.txt.gz
PGS004800
(migraine_PRSmixPlus_sas)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Migraine migraine disorder 2,968,987
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004800/ScoringFiles/PGS004800.txt.gz
PGS018986
(TPMI_340_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Migraine migraine disorder 154,713
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018986/ScoringFiles/PGS018986.txt.gz
PGS018987
(TPMI_340_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Migraine migraine disorder 356,947
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018987/ScoringFiles/PGS018987.txt.gz
PGS018988
(TPMI_340_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Migraine migraine disorder 19,422
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018988/ScoringFiles/PGS018988.txt.gz
PGS018989
(TPMI_340_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Migraine migraine disorder 983,774
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018989/ScoringFiles/PGS018989.txt.gz
PGS018990
(TPMI_340_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Migraine migraine disorder 959,731
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018990/ScoringFiles/PGS018990.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
PPM008903 PGS001281
(GBE_HC86)
 PSS004672|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Migraine — AUROC: 0.68314 [0.64175, 0.72454] R²: 0.04548
Incremental AUROC (full-covars): 0.00141
PGS R2 (no covariates): 7e-05
PGS AUROC (no covariates): 0.51212 [0.4664, 0.55784]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008904 PGS001281
(GBE_HC86)
 PSS004673|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Migraine — AUROC: 0.70929 [0.59332, 0.82526] Incremental AUROC (full-covars): 0.00197
R²: 0.0907
PGS R2 (no covariates): 0.00054
PGS AUROC (no covariates): 0.51635 [0.40666, 0.62605]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008905 PGS001281
(GBE_HC86)
 PSS004674|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Migraine — AUROC: 0.65031 [0.63271, 0.66791] R²: 0.03585
Incremental AUROC (full-covars): 0.00524
PGS R2 (no covariates): 0.00376
PGS AUROC (no covariates): 0.54846 [0.52849, 0.56843]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008906 PGS001281
(GBE_HC86)
 PSS004675|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Migraine — AUROC: 0.71746 [0.68326, 0.75166] R²: 0.07262
Incremental AUROC (full-covars): 0.00414
PGS R2 (no covariates): 0.0051
PGS AUROC (no covariates): 0.55594 [0.51785, 0.59403]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008907 PGS001281
(GBE_HC86)
 PSS004676|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Migraine — AUROC: 0.6514 [0.64118, 0.66162] R²: 0.03715
Incremental AUROC (full-covars): 0.00474
PGS R2 (no covariates): 0.0025
PGS AUROC (no covariates): 0.53959 [0.52853, 0.55066]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008908 PGS001282
(GBE_HC815)
 PSS004642|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE migraine — AUROC: 0.68512 [0.64613, 0.72411] PGS R2 (no covariates): 0.00032
R²: 0.04881
Incremental AUROC (full-covars): 0.00144
PGS AUROC (no covariates): 0.5084 [0.46412, 0.55269]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008909 PGS001282
(GBE_HC815)
 PSS004643|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE migraine — AUROC: 0.71233 [0.61741, 0.80724] R²: 0.08258
Incremental AUROC (full-covars): 0.00023
PGS R2 (no covariates): 3e-05
PGS AUROC (no covariates): 0.49923 [0.40691, 0.59154]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008910 PGS001282
(GBE_HC815)
 PSS004644|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE migraine — AUROC: 0.63835 [0.62244, 0.65426] R²: 0.03299
Incremental AUROC (full-covars): 0.00984
PGS R2 (no covariates): 0.00527
PGS AUROC (no covariates): 0.55358 [0.53641, 0.57074]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008911 PGS001282
(GBE_HC815)
 PSS004645|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE migraine — AUROC: 0.71231 [0.68018, 0.74443] R²: 0.07365
Incremental AUROC (full-covars): 0.00305
PGS R2 (no covariates): 0.00344
PGS AUROC (no covariates): 0.54217 [0.50698, 0.57735]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008912 PGS001282
(GBE_HC815)
 PSS004646|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE migraine — AUROC: 0.64859 [0.63934, 0.65784] R²: 0.03899
Incremental AUROC (full-covars): 0.00619
PGS R2 (no covariates): 0.0031
PGS AUROC (no covariates): 0.5408 [0.53085, 0.55076]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM021022 PGS004797
(migraine_PRSmix_eur)
 PSS011465|
European Ancestry|
9,462 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Migraine — — Incremental R2 (Full model versus model with only covariates): 0.003 [0.001, 0.005] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM021023 PGS004798
(migraine_PRSmix_sas)
 PSS011474|
South Asian Ancestry|
8,837 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Migraine — — Incremental R2 (Full model versus model with only covariates): 0.004 [0.001, 0.006] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM021024 PGS004799
(migraine_PRSmixPlus_eur)
 PSS011465|
European Ancestry|
9,462 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Migraine — — Incremental R2 (Full model versus model with only covariates): 0.019 [0.013, 0.024] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM021025 PGS004800
(migraine_PRSmixPlus_sas)
 PSS011474|
South Asian Ancestry|
8,837 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Migraine — — Incremental R2 (Full model versus model with only covariates): 0.011 [0.007, 0.016] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM037168 PGS018986
(TPMI_340_Lassosum2)
 PSS012889|
East Asian Ancestry|
18,664 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Migraine — AUROC: 0.76375 R²: 0.11662 sex, age, array, PCs 1-10 —
PPM037169 PGS018987
(TPMI_340_LDpred2)
 PSS012888|
East Asian Ancestry|
18,664 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Migraine — AUROC: 0.76372 R²: 0.11649 sex, age, array, PCs 1-10 —
PPM037170 PGS018988
(TPMI_340_MegaPRS)
 PSS012890|
East Asian Ancestry|
18,664 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Migraine — AUROC: 0.76013 R²: 0.11377 sex, age, array, PCs 1-10 —
PPM037171 PGS018989
(TPMI_340_PRS-CS)
 PSS012891|
East Asian Ancestry|
18,664 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Migraine — AUROC: 0.76286 R²: 0.11567 sex, age, array, PCs 1-10 —
PPM037172 PGS018990
(TPMI_340_SBayesR)
 PSS012892|
East Asian Ancestry|
18,664 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Migraine — AUROC: 0.76335 R²: 0.11547 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
PSS004672 — —
[
  • 148 cases
  • , 6,349 controls
]
 — African unspecified — UKB —
PSS004673 — —
[
  • 27 cases
  • , 1,677 controls
]
 — East Asian — UKB —
PSS004674 — —
[
  • 821 cases
  • , 24,084 controls
]
 — European non-white British ancestry UKB —
PSS004675 — —
[
  • 217 cases
  • , 7,614 controls
]
 — South Asian — UKB —
PSS004676 — —
[
  • 2,642 cases
  • , 64,783 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004642 — —
[
  • 169 cases
  • , 6,328 controls
]
 — African unspecified — UKB —
PSS004643 — —
[
  • 34 cases
  • , 1,670 controls
]
 — East Asian — UKB —
PSS004644 — —
[
  • 1,079 cases
  • , 23,826 controls
]
 — European non-white British ancestry UKB —
PSS004645 — —
[
  • 265 cases
  • , 7,566 controls
]
 — South Asian — UKB —
PSS004646 — —
[
  • 3,398 cases
  • , 64,027 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS011465 — — 9,462 individuals — European — AllofUs —
PSS012892 339.0, 346,G43, G44.00, G44.01, G44.02, G44.03, G44.04 —
[
  • 654 cases
  • , 18,010 controls
]
,
46.9 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012888 339.0, 346,G43, G44.00, G44.01, G44.02, G44.03, G44.04 —
[
  • 654 cases
  • , 18,010 controls
]
,
46.9 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012889 339.0, 346,G43, G44.00, G44.01, G44.02, G44.03, G44.04 —
[
  • 654 cases
  • , 18,010 controls
]
,
46.9 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012890 339.0, 346,G43, G44.00, G44.01, G44.02, G44.03, G44.04 —
[
  • 654 cases
  • , 18,010 controls
]
,
46.9 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012891 339.0, 346,G43, G44.00, G44.01, G44.02, G44.03, G44.04 —
[
  • 654 cases
  • , 18,010 controls
]
,
46.9 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS011474 — — 8,837 individuals — South Asian — G&H —