TABLE 3.
Top-rank CpG sets from the pregnancy exposure and cord blood DNAm analysis, n = 378
| CpG Site | β | SE | P Value | FDR P Value | Chromosome | Position | Gene | Relation to CpG Island |
|---|---|---|---|---|---|---|---|---|
| Maternal serum at 8 weeks gestation | ||||||||
| Maternal serum caffeine (comparing tertile 2 vs. tertile 1) | ||||||||
| cg14229247 | −0.01007 | 0.002071 | 1.16E-06 | 0.608595 | 9 | 100,745,139 | ANP32B | Island |
| cg19140548 | 0.009416 | 0.002032 | 3.58E-06 | 0.608595 | 10 | 105,552,406 | SH3PXD2A | |
| cg03609636 | −0.00767 | 0.001625 | 2.37E-06 | 0.608595 | 11 | 102,323,712 | TMEM123 | Island |
| cg13000180 | 0.01182 | 0.002473 | 1.75E-06 | 0.608595 | 16 | 3,355,450 | ZNF75A | Island |
| cg13780046 | −0.02103 | 0.004542 | 3.65E-06 | 0.608595 | 21 | 43,756,472 | ||
| Maternal serum caffeine (comparing tertile 3 vs. tertile 1) | ||||||||
| cg08651856 | 0.02689 | 0.005955 | 6.30E-06 | 0.397483 | 4 | 103,780,165 | UBE2D3 | |
| cg24441866 | 0.03135 | 0.007311 | 1.80E-05 | 0.397483 | 4 | 175,075,603 | LOC101928509 | |
| cg17684034 | −0.01438 | 0.003296 | 1.28E-05 | 0.397483 | 5 | 74,862,658 | POLK | |
| cg05164570 | 0.01445 | 0.002936 | 8.60E-07 | 0.397483 | 5 | 140,071,033 | HARS | Island |
| cg01252586 | −0.00429 | 0.000952 | 6.58E-06 | 0.397483 | 5 | 175,815,479 | NOP16; HIGD2A | Island |
| Maternal serum paraxanthine (≥LOD vs. <LOD) | ||||||||
| cg03133256 | −0.01691 | 0.003512 | 1.48E-06 | 0.61718 | 22 | 24,802,889 | SPECC1L | |
| cg05112617 | 0.009442 | 0.001908 | 7.46E-07 | 0.61718 | 3 | 93,698,932 | ARL13B | Island |
| cg07677273 | 0.01606 | 0.003938 | 4.56E-05 | 0.621864 | 4 | 37,004,924 | ||
| cg08679638 | −0.01315 | 0.003147 | 2.93E-05 | 0.621864 | 4 | 88,883,651 | ||
| cg17596409 | −0.01198 | 0.002925 | 4.23E-05 | 0.621864 | 4 | 153,186,305 | ||
| Maternal serum theobromine at 8 weeks gestation (comparing tertile 2 vs. tertile 1) | ||||||||
| cg09460369 | 0.028 | 0.005 | 1.43E-08 | 0.011927 | 8 | 61,429,249 | RAB2A | Island |
| cg14651896 | −0.012 | 0.002 | 2.67E-07 | 0.111267 | 9 | 124,094,730 | GSN | |
| cg22906451 | −0.014 | 0.003 | 4.22E-07 | 0.117129 | 19 | 1,994,824 | BTBD2 | South Shore |
| cg08151407 | 0.017 | 0.003 | 6.78E-07 | 0.14123 | 3 | 183,171,057 | LINC00888 | |
| cg15326613 | −0.018 | 0.004 | 2.56E-06 | 0.222618 | 6 | 114,132,612 | ||
| Maternal serum theobromine at 8 weeks gestation (comparing tertile 3 vs. tertile 1) | ||||||||
| cg00282267 | 0.03608 | 0.007114 | 3.95E-07 | 0.217159 | 7 | 36,803,916 | ||
| cg20400017 | 0.01518 | 0.003026 | 5.21E-07 | 0.217159 | 9 | 120,535,563 | ||
| cg03818021 | −0.0116 | 0.002421 | 1.66E-06 | 0.27671 | 5 | 1,798,716 | MRPL36 | North Shore |
| cg27468830 | 0.01561 | 0.003248 | 1.53E-06 | 0.27671 | 7 | 157,227,072 | ||
| cg18209808 | −0.02923 | 0.006053 | 1.38E-06 | 0.27671 | 12 | 27,993,787 | ||
| Pregnancy self-report | ||||||||
| Any type of caffeinated beverage (8 weeks gestation) | ||||||||
| cg26341453 | −0.0101 | 0.002095 | 1.44E-06 | 0.599156 | 1 | 28,593,732 | ||
| cg03424508 | −0.05267 | 0.01078 | 1.02E-06 | 0.599156 | 17 | 86,925 | South Shore | |
| cg05164540 | −0.01735 | 0.003965 | 1.21E-05 | 0.621971 | 5 | 107,896,573 | ||
| cg15754587 | 0.01422 | 0.003302 | 1.66E-05 | 0.621971 | 6 | 25,170,368 | ||
| cg22149610 | −0.00779 | 0.001812 | 1.74E-05 | 0.621971 | 6 | 31,857,034 | Island | |
| Any type of caffeinated beverage (12–36 weeks gestation) | ||||||||
| cg19954884 | −0.00869 | 0.001737 | 5.69E-07 | 0.198177 | 4 | 129,775,763 | JADE1 | |
| cg07791897 | −0.01494 | 0.003027 | 7.99E-07 | 0.198177 | 5 | 55,897,584 | ||
| cg22141918 | 0.01674 | 0.003414 | 9.51E-07 | 0.198177 | 14 | 24,539,803 | CPNE6 | |
| cg24179591 | −0.01066 | 0.002149 | 6.96E-07 | 0.198177 | 16 | 66,967,636 | FAM96B | North Shore |
| cg20646219 | 0.01083 | 0.002318 | 2.97E-06 | 0.412843 | 17 | 38,490,228 | RARA | |
Abbreviations: CpG, cytosine-guanine; DNAm, DNA methylation; FDR, false discovery rate; LOD, limit of detection.