| 1 | Cleft lip/palate | Enrichment | BMP4, MSX1, TP63 | 4.68 |
| 2 | Cleft lip and alveolus | Enrichment | MSX1, TP63 | 4.03 |
| 3 | Histiocytoid hemangioma | Enrichment | FOS, FOSB | 3.81 |
| 4 | Cleft upper lip | Enrichment | MSX1, TP63 | 3.81 |
| 5 | Septopreoptic holoprosencephaly | Enrichment | GAS1, GLI2 | 2.80 |
| 6 | Midline interhemispheric variant of holoprosencephaly | Enrichment | GAS1, GLI2 | 2.80 |
| 7 | Microform holoprosencephaly | Enrichment | GAS1, GLI2 | 2.74 |
| 8 | Lobar holoprosencephaly | Enrichment | GAS1, GLI2 | 2.74 |
| 9 | Alobar holoprosencephaly | Enrichment | GAS1, GLI2 | 2.69 |
| 10 | Semilobar holoprosencephaly | Enrichment | GAS1, GLI2 | 2.64 |
| 11 | Rapp-hodgkin syndrome | Enrichment | TP63 | 2.40 |
| 12 | Ankyloblepharon-ectodermal defects-cleft lip/palate | Enrichment | TP63 | 2.40 |
| 13 | Parietal foramina with cleidocranial dysplasia | Enrichment | MSX2 | 2.40 |
| 14 | Bamforth-lazarus syndrome | Enrichment | FOXE1 | 2.40 |
| 15 | T-cell immunodeficiency, congenital alopecia, and nail dystrophy | Enrichment | FOXN1 | 2.40 |
| 16 | Split-hand/foot malformation 4 | Enrichment | TP63 | 2.40 |
| 17 | Ankyloblepharon filiforme adnatum and cleft palate | Enrichment | TP63 | 2.40 |
| 18 | Charcot-marie-tooth disease, demyelinating, type 1d | Enrichment | EGR2 | 2.40 |
| 19 | Stargardt disease 4 | Enrichment | PROM1 | 2.40 |
| 20 | Skeletal defects, genital hypoplasia, and impaired intellectual development | Enrichment | ZBTB16 | 2.40 |
| 21 | Parietal foramina 1 | Enrichment | MSX2 | 2.40 |
| 22 | Adult syndrome | Enrichment | TP63 | 2.40 |
| 23 | Amelogenesis imperfecta, hypomaturation type, iia1 | Enrichment | KLK4 | 2.40 |
| 24 | Macular dystrophy, retinal, 2 | Enrichment | PROM1 | 2.40 |
| 25 | Culler-jones syndrome | Enrichment | GLI2 | 2.40 |
| 26 | T-cell immunodeficiency with thymic aplasia | Enrichment | FOXN1 | 2.40 |
| 27 | Ectodermal dysplasia 17 with or without limb malformations | Enrichment | LEF1 | 2.40 |
| 28 | T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant | Enrichment | FOXN1 | 2.40 |
| 29 | Immunodeficiency 69 | Enrichment | IFNG | 2.40 |
| 30 | Microphthalmia, syndromic 6 | Enrichment | BMP4 | 2.40 |
| 31 | Orofacial cleft 11 | Enrichment | BMP4 | 2.40 |
| 32 | Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3 | Enrichment | TP63 | 2.40 |
| 33 | Limb-mammary syndrome | Enrichment | TP63 | 2.40 |
| 34 | Craniosynostosis 2 | Enrichment | MSX2 | 2.40 |
| 35 | Holoprosencephaly 9 | Enrichment | GLI2 | 2.40 |
| 36 | Iron overload | Enrichment | BMP6 | 2.40 |
| 37 | Premature ovarian failure 21 | Enrichment | TP63 | 2.40 |
| 38 | Olmsted syndrome 2 | Enrichment | PERP | 2.40 |
| 39 | Retinitis pigmentosa 41 | Enrichment | PROM1 | 2.40 |
| 40 | Orofacial cleft 8 | Enrichment | TP63 | 2.40 |
| 41 | Thyroid cancer, nonmedullary, 4 | Enrichment | FOXE1 | 2.40 |
| 42 | Erythrokeratodermia variabilis et progressiva 7 | Enrichment | PERP | 2.40 |
| 43 | Diffuse palmoplantar keratoderma with painful fissures | Enrichment | DSG1 | 2.40 |
| 44 | Focal palmoplantar keratoderma with joint keratoses | Enrichment | DSG1 | 2.40 |
| 45 | Heritable thoracic aortic disease | Enrichment | SMAD4 | 2.40 |
| 46 | Amelogenesis imperfecta type 2a1 | Enrichment | KLK4 | 2.40 |
| 47 | Charcot-marie-tooth disease type 1d | Enrichment | EGR2 | 2.40 |
| 48 | Tp63-related disorders | Enrichment | TP63 | 2.40 |
| 49 | Diffuse palmoplantar keratoderma | Enrichment | DSG1 | 2.40 |
| 50 | Postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome | Enrichment | GLI2 | 2.40 |
| 51 | Ectrodactyly and ectodermal dysplasia without cleft lip/palate | Enrichment | LEF1 | 2.10 |
| 52 | Palmoplantar keratoderma i, striate, focal, or diffuse | Enrichment | DSG1 | 2.10 |
| 53 | Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 1 | Enrichment | TP63 | 2.10 |
| 54 | Myhre syndrome | Enrichment | SMAD4 | 2.10 |
| 55 | Camurati-engelmann disease 1 | Enrichment | TGFB1 | 2.10 |
| 56 | Kyphomelic dysplasia | Enrichment | CCN2 | 2.10 |
| 57 | Arrhythmogenic right ventricular dysplasia, familial, 11 | Enrichment | DSC2 | 2.10 |
| 58 | Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome | Enrichment | SMAD4 | 2.10 |
| 59 | Neuropathy, congenital hypomyelinating, 1, autosomal recessive | Enrichment | EGR2 | 2.10 |
| 60 | Orofacial cleft 5 | Enrichment | MSX1 | 2.10 |
| 61 | White-sutton syndrome | Enrichment | GLI2 | 2.10 |
| 62 | Witkop syndrome | Enrichment | MSX1 | 2.10 |
| 63 | Immunodeficiency, common variable, 12, with autoimmunity | Enrichment | NFKB1 | 2.10 |
| 64 | Spondyloepimetaphyseal dysplasia, li-shao-li type | Enrichment | CCN2 | 2.10 |
| 65 | Inflammatory bowel disease, immunodeficiency, and encephalopathy | Enrichment | TGFB1 | 2.10 |
| 66 | Bladder exstrophy | Enrichment | TP63 | 2.10 |
| 67 | Parietal foramina | Enrichment | MSX2 | 2.10 |
| 68 | Split hand-foot malformation | Enrichment | LEF1 | 2.10 |
| 69 | Hypotrichosis 6 | Enrichment | DSG4 | 2.10 |
| 70 | Camurati-engelmann disease | Enrichment | TGFB1 | 2.10 |
| 71 | Fissured tongue | Enrichment | TP63 | 2.10 |
| 72 | Growth delay due to insulin-like growth factor type 1 deficiency | Enrichment | IGF1 | 2.10 |
| 73 | Hereditary palmoplantar keratoderma | Enrichment | DSG1 | 2.10 |
| 74 | Common variable immunodeficiency 12 | Enrichment | NFKB1 | 2.10 |
| 75 | Juvenile polyposis syndrome | Enrichment | SMAD4 | 1.92 |
| 76 | Tuberous sclerosis 1 | Enrichment | IFNG | 1.92 |
| 77 | Hepatitis c virus | Enrichment | IFNG | 1.92 |
| 78 | Cone-rod dystrophy 12 | Enrichment | PROM1 | 1.92 |
| 79 | Tuberous sclerosis 2 | Enrichment | IFNG | 1.92 |
| 80 | Neonatal nephrocutaneous inflammatory syndrome | Enrichment | EGFR | 1.92 |
| 81 | Erythroderma, congenital, with palmoplantar keratoderma, hypotrichosis, and hyper-ige | Enrichment | DSG1 | 1.92 |
| 82 | Keratosis palmoplantaris striata | Enrichment | DSG1 | 1.92 |
| 83 | Mutilating palmoplantar keratoderma with periorificial keratotic plaques | Enrichment | PERP | 1.92 |
| 84 | Charcot-marie-tooth disease type 1 | Enrichment | EGR2 | 1.92 |
| 85 | Neonatal inflammatory skin and bowel disease | Enrichment | EGFR | 1.92 |
| 86 | Familial papillary or follicular thyroid carcinoma | Enrichment | FOXE1 | 1.92 |
| 87 | Robinow syndrome, autosomal dominant 1 | Enrichment | WNT5A | 1.80 |
| 88 | Microphthalmia, syndromic 3 | Enrichment | SOX2 | 1.80 |
| 89 | Congenital generalized lipodystrophy | Enrichment | FOS | 1.80 |
| 90 | Monilethrix | Enrichment | DSG4 | 1.80 |
| 91 | Orofacial cleft | Enrichment | FST | 1.80 |
| 92 | Autosomal dominant robinow syndrome | Enrichment | WNT5A | 1.80 |
| 93 | Orofacial clefting syndrome | Enrichment | FST | 1.80 |
| 94 | Pseudomyogenic hemangioendothelioma | Enrichment | FOSB | 1.80 |
| 95 | Hypertrophic neuropathy of dejerine-sottas | Enrichment | EGR2 | 1.70 |
| 96 | Arrhythmogenic right ventricular dysplasia, familial, 1 | Enrichment | DSC2 | 1.70 |
| 97 | Robinow syndrome, autosomal recessive 1 | Enrichment | WNT5A | 1.70 |
| 98 | Insulin-like growth factor i | Enrichment | IGF1 | 1.70 |
| 99 | Arrhythmogenic right ventricular dysplasia 1 | Enrichment | DSC2 | 1.70 |
| 100 | Diffuse cutaneous systemic sclerosis | Enrichment | CCN2 | 1.70 |
| 101 | Generalized juvenile polyposis/juvenile polyposis coli | Enrichment | SMAD4 | 1.70 |
| 102 | Idiopathic aplastic anemia | Enrichment | IFNG | 1.70 |
| 103 | Primary ovarian insufficiency | Enrichment | BMP6, TP63 | 1.64 |
| 104 | Cowden syndrome 1 | Enrichment | EGFR | 1.63 |
| 105 | Split-hand/foot malformation 1 | Enrichment | LEF1 | 1.63 |
| 106 | Anterior segment dysgenesis 5 | Enrichment | BMP4 | 1.63 |
| 107 | Inflammatory bowel disease 25, autosomal recessive | Enrichment | TGFB1 | 1.63 |
| 108 | Autosomal recessive robinow syndrome | Enrichment | WNT5A | 1.63 |
| 109 | Limited scleroderma | Enrichment | CCN2 | 1.63 |
| 110 | Il10-related early-onset inflammatory bowel disease | Enrichment | TGFB1 | 1.63 |
| 111 | Lung squamous cell carcinoma | Enrichment | EGFR | 1.63 |
| 112 | Hypothyroidism, congenital, nongoitrous, 2 | Enrichment | FOXE1 | 1.56 |
| 113 | Squamous cell carcinoma, head and neck | Enrichment | EGFR | 1.56 |
| 114 | Gallbladder cancer | Enrichment | SMAD4 | 1.56 |
| 115 | Hereditary hemorrhagic telangiectasia | Enrichment | SMAD4 | 1.56 |
| 116 | Common variable immunodeficiency | Enrichment | NFKB1 | 1.56 |
| 117 | Amelogenesis imperfecta type 2 | Enrichment | KLK4 | 1.56 |
| 118 | Hemochromatosis, type 1 | Enrichment | BMP6 | 1.50 |
| 119 | Leber congenital amaurosis 1 | Enrichment | PROM1 | 1.50 |
| 120 | Isolated split hand-split foot malformation | Enrichment | TP63 | 1.50 |
| 121 | Combined pituitary hormone deficiency | Enrichment | GLI2 | 1.50 |
| 122 | Tooth agenesis, selective, 1 | Enrichment | MSX1 | 1.45 |
| 123 | Familial isolated arrhythmogenic right ventricular dysplasia | Enrichment | DSC2 | 1.45 |
| 124 | Hypotrichosis simplex | Enrichment | DSG4 | 1.45 |
| 125 | Peters-plus syndrome | Enrichment | BMP4 | 1.41 |
| 126 | Ciliary dyskinesia, primary, 3 | Enrichment | NFKB1 | 1.41 |
| 127 | Aplastic anemia | Enrichment | IFNG | 1.41 |
| 128 | Stickler syndrome | Enrichment | BMP4 | 1.41 |
| 129 | Nanophthalmos | Enrichment | SOX2 | 1.37 |
| 130 | Lung non-small cell carcinoma | Enrichment | EGFR | 1.37 |
| 131 | Septooptic dysplasia | Enrichment | SOX2 | 1.33 |
| 132 | Renal hypodysplasia/aplasia 3 | Enrichment | BMP4 | 1.33 |
| 133 | Inherited isolated arrhythmogenic ventricular dysplasia, biventricular variant | Enrichment | DSC2 | 1.33 |
| 134 | Inherited isolated arrhythmogenic cardiomyopathy, dominant-left variant | Enrichment | DSC2 | 1.33 |
| 135 | Lip and oral cavity carcinoma | Enrichment | EGFR | 1.33 |
| 136 | Aortic valve disease 1 | Enrichment | DSG1 | 1.30 |
| 137 | Acute promyelocytic leukemia | Enrichment | ZBTB16 | 1.30 |
| 138 | Premature menopause | Enrichment | TP63 | 1.30 |
| 139 | Amelogenesis imperfecta | Enrichment | KLK4 | 1.30 |
| 140 | Lung cancer susceptibility 3 | Enrichment | EGFR | 1.26 |
| 141 | Inherited isolated arrhythmogenic cardiomyopathy, dominant-right variant | Enrichment | DSC2 | 1.26 |
| 142 | Isolated macular dystrophy | Enrichment | PROM1 | 1.26 |
| 143 | Male infertility with spermatogenesis disorder | Enrichment | TP63 | 1.24 |
| 144 | Arrhythmogenic right ventricular cardiomyopathy | Enrichment | DSC2 | 1.21 |
| 145 | Gliosarcoma | Enrichment | EGFR | 1.21 |
| 146 | Polycystic liver disease | Enrichment | DKK3 | 1.18 |
| 147 | Giant cell glioblastoma | Enrichment | EGFR | 1.18 |
| 148 | Autosomal dominant polycystic liver disease | Enrichment | DKK3 | 1.18 |
| 149 | Human immunodeficiency virus type 1 | Enrichment | IFNG | 1.16 |
| 150 | Charcot-marie-tooth disease type 4 | Enrichment | EGR2 | 1.16 |
| 151 | Arteriovenous malformations of the brain | Enrichment | EGFR | 1.14 |
| 152 | Macs syndrome | Enrichment | SOX2 | 1.12 |
| 153 | Craniosynostosis | Enrichment | GLI2 | 1.12 |
| 154 | Cardiomyopathy, dilated, 1a | Enrichment | DSC2 | 1.09 |
| 155 | Microphthalmia | Enrichment | SOX2 | 1.08 |
| 156 | Tooth agenesis | Enrichment | MSX1 | 1.08 |
| 157 | Skin disease | Enrichment | DSG1 | 1.08 |
| 158 | Precursor t-cell acute lymphoblastic leukemia | Enrichment | ZBTB16 | 1.06 |
| 159 | Pancreatic cancer | Enrichment | SMAD4 | 1.02 |
| 160 | Inherited cancer-predisposing syndrome | Enrichment | EGFR, SMAD4 | 1.01 |
| 161 | Bladder cancer | Enrichment | EGFR | 0.96 |
| 162 | Differentiated thyroid carcinoma | Enrichment | FOXE1 | 0.96 |
| 163 | Stargardt disease 1 | Enrichment | PROM1 | 0.95 |
| 164 | Lung cancer | Enrichment | EGFR | 0.92 |
| 165 | Cystic fibrosis | Enrichment | TGFB1 | 0.92 |
| 166 | Usher syndrome | Enrichment | PROM1 | 0.91 |
| 167 | Severe combined immunodeficiency | Enrichment | FOXN1 | 0.91 |
| 168 | Gastric cancer | Enrichment | SMAD4 | 0.80 |
| 169 | Familial thoracic aortic aneurysm and aortic dissection | Enrichment | SMAD4 | 0.79 |
| 170 | Thrombocytopenia | Enrichment | SMAD4 | 0.76 |
| 171 | Male infertility with azoospermia or oligozoospermia due to single gene mutation | Enrichment | GLI2 | 0.70 |
| 172 | Cone-rod dystrophy 2 | Enrichment | PROM1 | 0.62 |
| 173 | Autism | Enrichment | FOXN1 | 0.60 |
| 174 | Breast cancer | Enrichment | JUN | 0.59 |
| 175 | Colorectal cancer | Enrichment | SMAD4 | 0.53 |
| 176 | Leber plus disease | Enrichment | PROM1 | 0.50 |
| 177 | Ovarian cancer | Enrichment | EGFR | 0.48 |
| 178 | Retinitis pigmentosa | Enrichment | PROM1 | 0.24 |
| 179 | Hereditary retinal dystrophy | Enrichment | PROM1 | 0.16 |
| 180 | Fundus dystrophy | Enrichment | PROM1 | 0.16 |