Table 3. Significant phenotypes.
(A) Significant phenotypes with disease–genetic variant enrichments
specific to T2D subtype 1
PhenotypesGene symbolP
Albumin-to-creatinine ratiosACE1.00 × 10−27
Aspartyl phenylalanine levelsACE1.00 × 10−27
B cell countLAMB41.00 × 10−27
Chronic heart failureLEPR1.00 × 10−27
Crypt frequencySEMA3A1.00 × 10−27
DyslexiaCLSTN21.00 × 10−27
HypercholesterolemiaBTN2A11.00 × 10−27
Mannose-binding lectin levelsMBL21.00 × 10−27
Prominence of right endocanthionTMTC21.00 × 10−27
Retinol levelsFFAR41.00 × 10−27
Phosphorylated τ 181 protein levelsMTUS1, UNC5C5.53 × 10−3
Angiotensin-converting enzyme activityACE1.32 × 10−2
Diabetes mellitusBTN2A11.32 × 10−2
Entorhinal cortical volumeF13A11.32 × 10−2
Multiple system atrophySNCA1.32 × 10−2
N-acetylornithine levelsALMS11.32 × 10−2
OtosclerosisTGFB11.32 × 10−2
Pelvic organ prolapseZFAT1.32 × 10−2
Tanning abilityMC1R1.32 × 10−2
Vitamin D concentrationsGC1.32 × 10−2
Diabetic retinopathyPLXDC2, HS6ST32.32 × 10−2
Alanine transaminase levelsZNF8273.66 × 10−2
Diabetic nephropathyACE3.66 × 10−2
Left ventricular wall thicknessGRID13.66 × 10−2
Leptin receptorLEPR3.66 × 10−2
Forced expiratory volumeZSCAN31, TNS15.00 × 10−2
Platelet response to aspirin
intervention therapy
ZNF583, GLIS35.00 × 10−2
(B) Significant phenotypes with disease–genetic variant enrichments specific to
T2D subtype 2
PhenotypesGene symbolP
Alcohol and nicotine codependencePLEKHG11.00 × 10−27
Bleomycin sensitivitySAMD121.00 × 10−27
Epirubicin-induced adverse drug reactionsMCPH11.00 × 10−27
Follicular lymphomaSV2B1.00 × 10−27
Lactose intoleranceST51.00 × 10−27
Pronasale to left alare distanceCACNA2D31.00 × 10−27
Stem cell transplantationNLRP31.00 × 10−27
Geographic atrophyHTRA1, CFH6.57 × 10−4
BrainCDH47.58 × 10−3
Left ventricular internal diastolic dimensionsSLC35F17.58 × 10−3
Mean platelet volumeARHGEF37.58 × 10−3
Polypoidal choroidal vasculopathyCFH7.58 × 10−3
PsychosisZNF804A7.58 × 10−3
Suicidal behaviorGFRA17.58 × 10−3
Tanning abilityHERC27.58 × 10−3
Total τ protein levelsCDH47.58 × 10−3
Meningococcal diseaseTMPRSS15, CFHR3, CFH7.79 × 10−3
KeratoconusSOX5, MACROD21.76 × 10−2
MeningiomaCHN22.14 × 10−2
Polycystic ovary syndromeDENND1A2.14 × 10−2
Primary sclerosing cholangitisGAS72.14 × 10−2
Atrial fibrillationCAV1, HCN42.64 × 10−2
Age-related macular degenerationPLEKHA1, HTRA1, IL8, CFH3.09 × 10−2
Open-angle glaucomaADAMTSL1, CAV13.71 × 10−2
Phosphorylated τ 181 protein levelsCHN24.04 × 10−2
(C) Significant phenotypes with disease–genetic variant enrichments specific to
T2D subtype 3
PhenotypesGene symbolP
Gallbladder cancerCNTN4, DCC1.00 × 10−27
AllergyFHIT1.00 × 10−27
B cell chronic lymphocytic leukemiaCD381.00 × 10−27
Lymphoid interstitial pneumonitisFGF141.00 × 10−27
OsteoporosisALDH7A11.00 × 10−27
Peripartum cardiomyopathyAKAP131.00 × 10−27
RR intervalGPR1331.00 × 10−27
Spinocerebellar ataxia type 1ATXN11.00 × 10−27
Intraventricular septal thicknessEXT1, CERS61.65 × 10−3
Endometrial cancerSLC8A11.40 × 10−2
HIV-associated
neurocognitive disorders
SLC8A11.40 × 10−2
Response to statinASB181.40 × 10−2
Uterine leiomyomaTNRC6B1.40 × 10−2
Vitamin D concentrationsDAB11.40 × 10−2
Anxiety disordersSDK2, FHIT2.50 × 10−2
Cognitive declineCTNND23.86 × 10−2
DementiaABCA13.86 × 10−2
Estrone levelsESR13.86 × 10−2
Impaired play skillsDCC3.86 × 10−2
IntelligenceCNTN43.86 × 10−2
MyopiaMIPEP3.86 × 10−2
Plasma progranulin levelsDNAH113.86 × 10−2
Polycystic ovary syndromeTHADA3.86 × 10−2
Renal cell carcinomaITPR23.86 × 10−2
Theta power of electroencephalogramST6GALNAC33.86 × 10−2
Central corneal thicknessCOL5A1, FNDC3B4.00 × 10−2
Atrial fibrillationC9orf3, SYNE25.00 × 10−2
DepressionFHIT, BICC15.00 × 10−2