Table 4.
The top 50 differentially methylated CpGs in whole blood, ordered by q-value, when comparing the high and control burden groups
| CpG | CHR | Gene | Regression Coeff. | pval | qval |
|---|---|---|---|---|---|
| cg13442689 | 7 | PTPRN2 | 0.037 | 2.1E-07 | 0.100 |
| cg04344875 | 7 | MEST,MESTIT1 | 0.019 | 8.3E-07 | 0.179 |
| cg06353830 | 1 | −0.024 | 1.3E-06 | 0.179 | |
| cg07064673 | 11 | HCCA2 | 0.016 | 1.5E-06 | 0.179 |
| cg02500300 | 4 | STOX2 | 0.014 | 2.1E-06 | 0.204 |
| cg19558802 | 15 | GLDN | 0.047 | 3.1E-06 | 0.248 |
| cg23154021 | 12 | −0.059 | 3.7E-06 | 0.259 | |
| cg14950515 | 4 | −0.048 | 4.5E-06 | 0.273 | |
| cg24393602 | 6 | GSTA4 | 0.018 | 6.3E-06 | 0.337 |
| cg06713076 | 17 | −0.020 | 7.4E-06 | 0.354 | |
| cg04507925 | 2 | UNC80 | −0.030 | 9.1E-06 | 0.354 |
| cg20697519 | 1 | SLAMF8 | 0.021 | 1.0E-05 | 0.354 |
| cg03450733 | X | ARX | −0.061 | 1.0E-05 | 0.354 |
| cg12948543 | 14 | PACS2 | 0.014 | 1.2E-05 | 0.354 |
| cg08084655 | 17 | BTBD17 | −0.034 | 1.3E-05 | 0.354 |
| cg00152946 | 10 | −0.017 | 1.3E-05 | 0.354 | |
| cg18898267 | 8 | −0.050 | 1.3E-05 | 0.354 | |
| cg20845970 | 8 | −0.022 | 1.4E-05 | 0.354 | |
| cg21461300 | 13 | RASA3 | −0.038 | 1.5E-05 | 0.354 |
| cg08721112 | 1 | −0.086 | 1.5E-05 | 0.354 | |
| cg21355100 | 19 | ZNF555 | 0.024 | 1.5E-05 | 0.354 |
| cg10881110 | 1 | SLC25A34 | 0.020 | 1.7E-05 | 0.360 |
| cg06534800 | 5 | DOK3 | 0.019 | 1.7E-05 | 0.360 |
| cg24352317 | X | LOC729609 | −0.032 | 2.1E-05 | 0.425 |
| cg24757937 | 14 | SIX1 | −0.036 | 2.3E-05 | 0.425 |
| cg22258713 | 8 | 0.048 | 2.3E-05 | 0.425 | |
| cg24851684 | 6 | DHX16 | 0.017 | 2.4E-05 | 0.425 |
| cg00893368 | 13 | RASA3 | −0.025 | 2.5E-05 | 0.436 |
| cg11576274 | 1 | −0.048 | 2.7E-05 | 0.449 | |
| cg27590787 | X | 0.089 | 2.9E-05 | 0.476 | |
| cg26708559 | 7 | MEST,MESTIT1 | 0.017 | 3.1E-05 | 0.477 |
| cg16204066 | 6 | ITPR3 | −0.024 | 3.2E-05 | 0.477 |
| cg06439589 | X | SSR4 | 0.014 | 3.3E-05 | 0.477 |
| cg12905592 | 12 | FMNL3 | 0.020 | 3.8E-05 | 0.477 |
| cg08772163 | 13 | ARL11 | 0.013 | 4.1E-05 | 0.477 |
| cg22741244 | 2 | KLHL30 | −0.027 | 4.1E-05 | 0.477 |
| cg11646505 | 6 | 0.013 | 4.2E-05 | 0.477 | |
| cg03290530 | 3 | 0.045 | 4.2E-05 | 0.477 | |
| cg08132116 | 3 | NICN1 | 0.015 | 4.2E-05 | 0.477 |
| cg21032058 | 14 | TMEM63C | 0.012 | 4.3E-05 | 0.477 |
| cg00329180 | 16 | ANKRD11 | 0.020 | 4.4E-05 | 0.477 |
| cg00044796 | 1 | −0.105 | 4.7E-05 | 0.477 | |
| cg13036944 | 3 | 0.013 | 4.7E-05 | 0.477 | |
| cg02184697 | 16 | KREMEN2 | −0.050 | 4.8E-05 | 0.477 |
| cg05825400 | 17 | ABR | 0.030 | 5.0E-05 | 0.477 |
| cg26114595 | 17 | EFCAB5 | 0.019 | 5.0E-05 | 0.477 |
| cg01987515 | 2 | COPS7B | 0.010 | 5.2E-05 | 0.477 |
| cg17733084 | 1 | NEXN | −0.014 | 5.3E-05 | 0.477 |
| cg22671717 | 1 | −0.103 | 5.4E-05 | 0.477 | |
| cg26289712 | 8 | 0.016 | 5.4E-05 | 0.477 |
Data generated from a linear model with empirical Bayes estimation, which we used for the whole blood DNA methylation beta value comparisons between the Ranch Hand veterans with high serum TCDD levels (n = 15) and the control group (n = 12). The q-value was calculated using the Benjamini-Hochberg method. The regression coefficient identifies the direction of methylation change between the burden groups and was determined via the model we constructed. Genes associated with each CpG are also given in the table