Table 3.
51 differentially methylated loci associated with TNEs in the discovery meta-analysis that were replicated in the validation meta-analysis
|
Discovery meta-analysis |
Validation meta-analysis |
||||||||
|---|---|---|---|---|---|---|---|---|---|
| Probe_ID | Chr | Mapinfoa | Gene | Estimateb | SE | p value | Estimateb | SE | p value |
| cg05575921 | 5 | 373378 | AHRR | −0.0425 | 0.0022 | 1.52 × 10−84 | −0.0200 | 0.0033 | 9.90 × 10−10 |
| cg23576855 | 5 | 373299 | AHRR | −0.0444 | 0.0030 | 1.82 × 10−50 | −0.0216 | 0.0044 | 7.72 × 10−7 |
| cg03636183 | 19 | 17000585 | F2RL3 | −0.0276 | 0.0019 | 8.49 × 10−48 | −0.0182 | 0.0027 | 1.60 × 10−11 |
| cg17739917 | 17 | 38477572 | RARA | −0.0205 | 0.0015 | 2.50 × 10−44 | −0.0163 | 0.0028 | 4.22 × 10−9 |
| cg21161138 | 5 | 399360 | AHRR | −0.0156 | 0.0011 | 2.99 × 10−43 | −0.0086 | 0.0018 | 1.99 × 10−6 |
| cg19859270 | 3 | 98251294 | GPR15 | −0.0053 | 0.0004 | 3.80 × 10−41 | −0.0031 | 0.0007 | 8.45 × 10−6 |
| cg01940273 | 2 | 233284934 | 2q37.1 | −0.0165 | 0.0012 | 6.41 × 10−40 | −0.0076 | 0.0020 | 9.17 × 10−5 |
| cg26703534 | 5 | 377358 | AHRR | −0.0118 | 0.0009 | 4.74 × 10−38 | −0.0072 | 0.0017 | 2.22 × 10−5 |
| cg25845814 | 14 | 74224613 | MIR4505;ELMSAN1 | −0.0074 | 0.0006 | 4.93 × 10−36 | −0.0053 | 0.0011 | 1.46 × 10−6 |
| cg25648203 | 5 | 395444 | AHRR | −0.0117 | 0.0010 | 2.79 × 10−30 | −0.0084 | 0.0017 | 7.23 × 10−7 |
| cg02978227 | 3 | 98292027 | 3q11.2 | −0.0055 | 0.0005 | 2.45 × 10−29 | −0.0032 | 0.0007 | 6.90 × 10−6 |
| cg03329539 | 2 | 233283329 | 2q37.1 | −0.0116 | 0.0011 | 3.22 × 10−26 | −0.0085 | 0.0019 | 9.88 × 10−6 |
| cg07741821 | 7 | 26577897 | KIAA0087 | −0.0130 | 0.0012 | 8.25 × 10−26 | −0.0077 | 0.0019 | 7.00 × 10−5 |
| cg05086879 | 22 | 39861490 | MGAT3 | −0.0099 | 0.0010 | 2.26 × 10−25 | −0.0079 | 0.0015 | 1.97 × 10−7 |
| cg21911711 | 19 | 16998668 | F2RL3 | −0.0115 | 0.0012 | 3.39 × 10−22 | −0.0104 | 0.0021 | 7.55 × 10−7 |
| cg16841366 | 2 | 233286192 | 2q37.1 | −0.0233 | 0.0024 | 5.90 × 10−22 | −0.0126 | 0.0032 | 9.52 × 10−5 |
| cg02657160 | 3 | 98311063 | CPOX | −0.0049 | 0.0005 | 1.29 × 10−20 | −0.0035 | 0.0009 | 5.29 × 10−5 |
| cg26768182 | 9 | 134272679 | 9q34.13 | −0.0061 | 0.0007 | 3.47 × 10−20 | −0.0049 | 0.0012 | 6.50 × 10−5 |
| cg09935388 | 1 | 92947588 | GFI1 | −0.0212 | 0.0023 | 3.48 × 10−20 | −0.0156 | 0.0032 | 1.12 × 10−6 |
| cg23161492 | 15 | 90357202 | ANPEP | −0.0145 | 0.0016 | 9.59 × 10−19 | −0.0108 | 0.0024 | 9.10 × 10−6 |
| cg11660018 | 11 | 86510915 | PRSS23 | −0.0106 | 0.0012 | 3.89 × 10−18 | −0.0084 | 0.0019 | 1.52 × 10−5 |
| cg04180924 | 3 | 98272064 | 3q11.2 | −0.0026 | 0.0003 | 4.44 × 10−18 | −0.0027 | 0.0005 | 1.09 × 10−8 |
| cg22812571 | 2 | 233286229 | 2q37.1 | −0.0181 | 0.0021 | 7.59 × 10−18 | −0.0131 | 0.0028 | 3.91 × 10−6 |
| cg12876356 | 1 | 92946825 | GFI1 | −0.0117 | 0.0014 | 1.92 × 10−16 | −0.0063 | 0.0015 | 3.14 × 10−5 |
| cg22675726 | 18 | 3179889 | MYOM1 | −0.0139 | 0.0017 | 5.23 × 10−16 | −0.0144 | 0.0035 | 3.43 × 10−5 |
| cg04551776 | 5 | 393366 | AHRR | −0.0065 | 0.0008 | 2.75 × 10−15 | −0.0048 | 0.0012 | 1.09 × 10−4 |
| cg10765427 | 19 | 17005225 | CPAMD8 | −0.0058 | 0.0007 | 1.25 × 10−14 | −0.0046 | 0.0011 | 4.87 × 10−5 |
| cg23079012 | 2 | 8343710 | 2p25.1 | −0.0070 | 0.0009 | 2.47 × 10−14 | −0.0031 | 0.0007 | 2.91 × 10−5 |
| cg15159987 | 19 | 17003890 | CPAMD8 | −0.0067 | 0.0009 | 2.49 × 10−14 | −0.0060 | 0.0012 | 1.76 × 10−6 |
| cg14466441 | 6 | 11392193 | 6p24.2 | −0.0047 | 0.0006 | 4.30 × 10−14 | −0.0041 | 0.0009 | 1.20 × 10−5 |
| cg25061445 | 15 | 57912784 | GCOM1;MYZAP | −0.0099 | 0.0014 | 2.68 × 10−13 | −0.0102 | 0.0025 | 6.09 × 10−5 |
| cg06035956 | 5 | 379099 | AHRR | −0.0016 | 0.0002 | 4.27 × 10−13 | −0.0015 | 0.0004 | 7.80 × 10−5 |
| cg22441770 | 1 | 153929592 | CRTC2 | −0.0049 | 0.0007 | 1.18 × 10−11 | −0.0056 | 0.0011 | 6.28 × 10−7 |
| cg09098393 | 8 | 55423202 | 8q11.23 | −0.0099 | 0.0015 | 3.26 × 10−11 | −0.0116 | 0.0028 | 2.92 × 10−5 |
| cg07390844 | 18 | 72935911 | TSHZ1 | −0.0095 | 0.0014 | 5.29 × 10−11 | −0.0093 | 0.0024 | 9.34 × 10−5 |
| cg09842685 | 12 | 4492769 | 12p13.32 | −0.0065 | 0.001 | 1.36 × 10−10 | −0.0084 | 0.0014 | 2.01 × 10−9 |
| cg20684110 | 10 | 64565750 | ADO | −0.008 | 0.0013 | 4.00 × 10−10 | −0.0071 | 0.0017 | 1.91 × 10−5 |
| cg13849276 | 17 | 41328544 | NBR1 | −0.0111 | 0.0018 | 7.79 × 10−10 | −0.0096 | 0.0023 | 3.74 × 10−5 |
| cg23110422 | 21 | 40182073 | ETS2 | −0.0055 | 0.0009 | 7.82 × 10−10 | −0.0065 | 0.0014 | 3.93 × 10−6 |
| cg13177778 | 11 | 92900159 | SLC36A4 | −0.0084 | 0.0014 | 1.80 × 10−9 | −0.009 | 0.0022 | 3.82 × 10−5 |
| cg01005506 | 10 | 64565768 | ADO | −0.0071 | 0.0012 | 9.35 × 10−9 | −0.0076 | 0.002 | 1.16 × 10−4 |
| cg26237233 | 11 | 80782064 | 11q14.1 | −0.0057 | 0.001 | 9.40 × 10−9 | −0.0064 | 0.0015 | 1.36 × 10−5 |
| cg11931220 | 12 | 49276387 | 12q13.12 | −0.0069 | 0.0012 | 1.16 × 10−8 | −0.008 | 0.0019 | 2.23 × 10−5 |
| cg10062919 | 17 | 38503802 | RARA | −0.0034 | 0.0006 | 1.55 × 10−8 | −0.0035 | 0.0008 | 2.02 × 10−5 |
| cg15829114 | 14 | 53617878 | DDHD1 | −0.0054 | 0.001 | 1.66 × 10−8 | −0.0049 | 0.0012 | 7.00 × 10−5 |
| cg07978331 | 16 | 75046041 | ZNRF1 | −0.0073 | 0.0013 | 1.96 × 10−8 | −0.0079 | 0.0019 | 1.96 × 10−5 |
| cg05753553 | 17 | 2689486 | 17p13.3 | 0.0058 | 0.0011 | 3.02 × 10−8 | 0.0076 | 0.0017 | 5.57 × 10−6 |
| cg01481251 | 11 | 32912719 | 11p13 | −0.0045 | 0.0008 | 3.57 × 10−8 | −0.0051 | 0.0011 | 4.55 × 10−6 |
| cg17547179 | 7 | 45068955 | CCM2 | −0.0049 | 0.0009 | 3.67 × 10−8 | −0.0059 | 0.0014 | 1.94 × 10−5 |
| cg14034325 | 10 | 43891459 | HNRNPF | −0.0076 | 0.0014 | 4.74 × 10−8 | −0.0078 | 0.002 | 8.47 × 10−5 |
| cg10711136 | 11 | 86515053 | PRSS23 | −0.0065 | 0.0012 | 4.81 × 10−8 | −0.0084 | 0.002 | 1.81 × 10−5 |
Discovery genome-wide significance threshold: p < 9 × 10−8.
Validation Bonferroni-corrected significance threshold: p < 1.23 × 10−4 (p = 0.05/408).
Results are ordered by statistical significance in the discovery meta-analysis.
a
Chromosomal coordinates based on GRCh37.
b
Parameter estimate representing the change in methylation β value per one log-unit increase in TNEs.