Table 3.
Genes associated with risk of TGCT based on analysis of all SNPs in each gene
| GENE | N SNPs* | perm-p# | q-value§ |
|---|---|---|---|
| MTHFR | 13 | 3×10−5 | 8.4×10−4 |
| MECP2 | 4 | 1.4×10−4 | 2×10−3 |
| ZBTB4 | 7 | 3.2×10−3 | 0.03 |
| AHCY | 4 | 0.05 | 0.35 |
| MBD3L1 | 5 | 0.07 | 0.35 |
| SHMT1 | 8 | 0.1 | 0.35 |
| MAT1A | 14 | 0.1 | 0.35 |
| DNMT3L | 16 | 0.1 | 0.35 |
| DNMT1 | 8 | 0.17 | 0.42 |
| MAT2B | 9 | 0.18 | 0.42 |
| DNMT3B | 8 | 0.19 | 0.42 |
| ZBTB38 | 4 | 0.19 | 0.42 |
| UHRF1 | 13 | 0.20 | 0.42 |
| MTRR | 25 | 0.25 | 0.46 |
| TET2 | 9 | 0.26 | 0.46 |
| MBD2 | 10 | 0.27 | 0.46 |
| CBS | 17 | 0.30 | 0.50 |
| TET3 | 11 | 0.44 | 0.69 |
| MBD3 | 4 | 0.53 | 0.75 |
| BHMT | 13 | 0.53 | 0.75 |
| DNMT3A | 18 | 0.56 | 0.75 |
| MAT2A | 4 | 0.59 | 0.75 |
| TET1 | 7 | 0.65 | 0.76 |
| MBD2 | 7 | 0.65 | 0.76 |
| CTCF | 3 | 0.76 | 0.85 |
| MTR | 8 | 0.81 | 0.87 |
| MBD4 | 3 | 0.94 | 0.96 |
| GADD45b | 8 | 0.96 | 0.96 |
*
Number of SNPs tested within a gene
#
Gene level p-value computed by MAGMA after 100,000 permutations
§
Gene level q-value calculated on permutation p-value