Table 3.
List of hypomethylated CpG/CHH/CHG sites in the gene body/promoter/other chromosomal region of genes from high maternal folic acid diet that were significantly altered after multiple testing corrections.
| Chromosome | Start | End | Gene | Total CpG | Total CpG | Methylation | P-value | Adj P-value |
|---|---|---|---|---|---|---|---|---|
| LMFA | HMFA | difference | ||||||
| MALE | ||||||||
| CpG | ||||||||
| Chr2 | 70926781 | 70926782 | Dcaf17 | 12 | 8 | −1.00 | 7.9384E-06 | 0.028133219 |
| Chr3 | 51477712 | 51477713 | Mgst2 | 16 | 15 | −0.73 | 1.6121E-05 | 0.045534315 |
| Chr5 | 111715613 | 111715614 | Ttc28 | 46 | 19 | −0.79 | 1.95557E-09 | 3.9055E-05 |
| Chr10 | 79393579 | 79393580 | Arid3a | 18 | 12 | −0.83 | 2.1967E-06 | 0.010935514 |
| Chr11 | 69574236 | 69574237 | Amac1 | 42 | 15 | −0.80 | 2.10416E-08 | 0.000279056 |
| Chr11 | 89384648 | 89384649 | Ankfn1 | 16 | 19 | −0.74 | 9.65017E-06 | 0.032243587 |
| Chr12 | 109176310 | 109176311 | Bcl11b | 10 | 31 | −0.77 | 1.73473E-05 | 0.04752513 |
| Chr13 | 24228093 | 24228094 | Lrrc16a | 13 | 16 | −0.86 | 3.07969E-06 | 0.014240168 |
| Chr17 | 11729485 | 11729486 | Park2 | 10 | 10 | −1.00 | 1.08251E-05 | 0.034194413 |
| CHH | ||||||||
| Chr5 | 150366342 | 150366343 | Wdr95 | 27 | 32 | −0.85 | 1.21698E-12 | 7.55036E-06 |
| Chr6 | 119463258 | 119463259 | Wnt5b | 16 | 43 | −0.69 | 1.56071E-08 | 0.002104991 |
| Chr8 | 119603496 | 119603497 | Pkd1l2 | 25 | 56 | −0.60 | 7.02256E-09 | 0.001146559 |
| Chr9 | 107166117 | 107166118 | Mapkapk3 | 24 | 39 | −0.65 | 2.17476E-07 | 0.020757812 |
| Chr16 | 6736334 | 6736335 | Rbfox1 | 26 | 36 | −0.71 | 4.2963E-09 | 0.000740418 |
| 0.00 | ||||||||
| CHG | 0.00 | |||||||
| Chr4 | 43744421 | 43744422 | 5430416O09Rik | 38 | 79 | −0.66 | 1.89728E-11 | 4.03799E-05 |
| Chr9 | 103033308 | 103033309 | Rab6b | 23 | 37 | −0.65 | 9.21745E-09 | 0.00159268 |
| Chr9 | 104021165 | 104021166 | Acad11 | 38 | 72 | −0.58 | 2.74934E-11 | 4.03799E-05 |
| Chr11 | 118130307 | 118130308 | Usp36 | 38 | 51 | −0.55 | 2.20911E-10 | 7.42648E-05 |
| Chr16 | 15797072 | 15797073 | Prkdc | 8 | 26 | −1.00 | 5.50776E-08 | 0.006775161 |
| FEMALE | ||||||||
| CpG | ||||||||
| Chr1a | 39592922 | 39592923 | D1Bwg0212e | 46 | 12 | −0.72 | 7.29815E-06 | 0.034293206 |
| Chr2 | 54854875 | 54854876 | Galnt13 | 40 | 10 | −0.85 | 7.79574E-07 | 0.005370225 |
| Chr3 | 152572664 | 152572665 | St6galnac5 | 46 | 10 | −0.76 | 1.32097E-06 | 0.008651764 |
| Chr5 | 150883968 | 150883969 | Rxfp2 | 52 | 6 | −0.92 | 5.18834E-06 | 0.026484159 |
| Chr5 | 4009104 | 4009105 | Akap9 | 47 | 8 | −0.87 | 2.4664E-06 | 0.014583234 |
| Chr7 | 13564506 | 13564507 | Zfp446 | 17 | 6 | −1.00 | 9.90619E-06 | 0.043500018 |
| Chr7 | 142277612 | 142277613 | Dock1 | 49 | 15 | −0.71 | 2.05041E-08 | 0.000206849 |
| Chr8a | 73985459 | 73985460 | Abhd8 | 66 | 11 | −0.76 | 1.60125E-06 | 0.01005433 |
| Chr9 | 45614148 | 45614149 | Cep164 | 41 | 15 | −0.80 | 8.14852E-10 | 1.23014E-05 |
| Chr9 | 65575164 | 65575165 | Zfp609 | 35 | 8 | −0.75 | 4.59283E-06 | 0.024030758 |
| Chr11 | 100924353 | 100924354 | Atp6v0a1 | 40 | 6 | −0.95 | 2.98928E-06 | 0.016967907 |
| Chr11 | 63783989 | 63783990 | Cox10 | 24 | 12 | −0.92 | 7.27024E-08 | 0.00063948 |
| Chr11 | 118386794 | 118386795 | Rbfox3 | 33 | 10 | −0.82 | 4.17663E-06 | 0.02232177 |
| Chr11 | 70466348 | 70466349 | Pfn1 | 71 | 18 | −0.75 | 3.48721E-09 | 4.17015E-05 |
| Chr11 | 101045277 | 101045278 | Cntnap1 | 84 | 16 | −0.71 | 4.67003E-08 | 0.00043033 |
| Chr13 | 115629726 | 115629727 | Itga2 | 52 | 14 | −0.70 | 1.73075E-06 | 0.010740731 |
| Chr15 | 73386877 | 73386878 | Dennd3 | 42 | 6 | −0.95 | 2.28171E-06 | 0.013758747 |
| Chr15 | 76684078 | 76684079 | Zfp251 | 43 | 7 | −0.71 | 9.91146E-06 | 0.043500018 |
| Chr17 | 26145026 | 26145027 | Rab11fip3 | 35 | 6 | −1.00 | 2.22401E-07 | 0.00174687 |
| Chr17 | 34201190 | 34201191 | Col11a2 | 69 | 10 | −0.71 | 4.42664E-06 | 0.023265511 |
| Chr18 | 64349640 | 64349641 | 1700091E21Rik | 60 | 8 | −0.72 | 6.76961E-06 | 0.032675219 |
| ChrX | 130978215 | 130978216 | Drp2 | 42 | 6 | −0.95 | 2.28171E-06 | 0.013758747 |
| CHG | ||||||||
| Chr17a | 39981459 | 39981460 | Rn45s | 215 | 1801 | −0.32 | 3.15966E-11 | 0.000127773 |
| OTHER CHROMOSOMAL REGIONS | ||||||||
| MALE | ||||||||
| CpG | ||||||||
| Chr4 | 114927822 | 114927823 | 19 | 16 | −1.00 | 2.4631E-10 | 1.6251E-05 | |
| Chr4 | 70356713 | 70356714 | 11 | 8 | −1.00 | 1.32307E-05 | 0.039611439 | |
| Chr4 | 33145068 | 33145069 | 22 | 23 | −0.74 | 1.15388E-07 | 0.001082193 | |
| Chr6 | 22702718 | 22702719 | 20 | 38 | −0.79 | 1.68255E-09 | 3.40026E-05 | |
| Chr8 | 23561782 | 23561783 | 10 | 9 | −1.00 | 1.08251E-05 | 0.034194413 | |
| Chr8 | 125951782 | 125951783 | 6 | 15 | −1.00 | 1.84284E-05 | 0.049033126 | |
| Chr8 | 15641954 | 15641955 | 33 | 10 | −0.87 | 1.72635E-07 | 0.001510603 | |
| Chr9 | 49862607 | 49862608 | 10 | 10 | −1.00 | 1.08251E-05 | 0.034194413 | |
| Chr10 | 12602192 | 12602193 | 17 | 8 | −1.00 | 9.24578E-07 | 0.005834628 | |
| Chr10 | 123989391 | 123989392 | 17 | 35 | −0.83 | 4.59988E-09 | 7.96787E-05 | |
| Chr12 | 44576005 | 44576006 | 19 | 14 | −0.80 | 3.041E-06 | 0.014104497 | |
| Chr12 | 68850704 | 68850705 | 31 | 14 | −0.76 | 1.20506E-06 | 0.007029716 | |
| Chr14 | 13972178 | 13972179 | 44 | 9 | −0.84 | 4.38892E-07 | 0.003296639 | |
| Chr15 | 31799762 | 31799763 | 14 | 16 | −0.81 | 4.79293E-06 | 0.019439463 | |
| Chr16 | 55473911 | 55473912 | 24 | 11 | −0.78 | 1.52675E-05 | 0.043927676 | |
| Chr17 | 84101994 | 84101995 | 10 | 10 | −1.00 | 1.08251E-05 | 0.034194413 | |
| Chr17 | 40509054 | 40509055 | 26 | 26 | −0.73 | 1.66363E-07 | 0.001486366 | |
| CHH | ||||||||
| Chr4 | 62532417 | 62532418 | 30 | 18 | −0.80 | 3.6826E-08 | 0.004662758 | |
| Chr16 | 39097237 | 39097238 | 47 | 34 | −0.70 | 4.56498E-11 | 5.49912E-05 | |
| Chr18 | 53985910 | 53985911 | 27 | 30 | −0.63 | 6.04117E-08 | 0.007071799 | |
| CHG | ||||||||
| Chr4 | 44486603 | 44486604 | 24 | 72 | −0.53 | 1.53357E-07 | 0.017325988 | |
| Chr8 | 97707113 | 97707114 | 31 | 43 | −0.52 | 4.46831E-08 | 0.006250153 | |
| Chr8 | 91367262 | 91367263 | 39 | 56 | −0.46 | 5.61123E-09 | 0.001030159 | |
| Chr10 | 93725790 | 93725791 | 84 | 53 | −0.46 | 1.1065E-10 | 7.42648E-05 | |
| Chr11 | 101785985 | 101785986 | 26 | 44 | −0.54 | 4.99742E-08 | 0.006672518 | |
| FEMALE | ||||||||
| CpG | ||||||||
| Chr1 | 72001078 | 72001079 | 32 | 8 | −0.75 | 7.29474E-06 | 0.034293206 | |
| Chr2 | 178977613 | 178977614 | 52 | 10 | −0.88 | 7.44799E-08 | 0.000649745 | |
| Chr3 | 69055711 | 69055712 | 66 | 8 | −0.85 | 2.90337E-06 | 0.016568628 | |
| Chr5 | 48149488 | 48149489 | 54 | 10 | −0.80 | 1.01668E-08 | 0.00011098 | |
| Chr7 | 76060069 | 76060070 | 43 | 10 | −0.77 | 9.4751E-06 | 0.042282364 | |
| Chr8 | 4203056 | 4203057 | 66 | 6 | −0.91 | 5.91402E-06 | 0.029620167 | |
| Chr8 | 66000281 | 66000282 | 61 | 8 | −0.72 | 6.1866E-06 | 0.030412915 | |
| Chr16 | 22049549 | 22049550 | 26 | 14 | −0.71 | 1.1809E-06 | 0.007855174 | |
| Chr18 | 83282753 | 83282754 | 95 | 9 | −0.83 | 9.90991E-08 | 0.000823993 | |
| Chr18 | 67611225 | 67611226 | 62 | 10 | −0.74 | 9.90604E-06 | 0.043500018 | |
| Chr19 | 45266101 | 45266102 | 30 | 18 | −0.80 | 3.6826E-08 | 0.00034839 | |
a
Methylation exclusively in the CpG island; HMFA, high maternal folic acid; LMFA, low maternal folic acid. CHH, CHG where H can be A, T or G.