Table 3.
Chr | SNP | Position (bp) | MWAS | Replication | Gene | |||||
---|---|---|---|---|---|---|---|---|---|---|
T | P-value | q-value | Effect | T | P-value | Effect | ||||
2 | rs605832 | 31454545 | −5.65 | 2.0E-08 | 0.010 | −0.301 | −0.91 | 1.8E-01 | −0.232 | |
3 | rs9827299 | 71353372 | −6.59 | 6.3E-11 | 0.000 | −0.351 | 0.79 | 7.8E-01 | 0.202 | FOXP1 |
3 | rs3796293 | 190332093 | −5.49 | 4.7E-08 | 0.015 | −0.292 | −2.88 | 3.0E-03 | −0.732 | IL1RAP |
15 | rs56153788 | 86170992 | −5.33 | 1.1E-07 | 0.028 | −0.284 | 0.70 | 7.5E-01 | 0.177 | AKAP13 |
16 | rs2542671 | 54209836 | −5.26 | 1.6E-07 | 0.032 | −0.280 | −0.06 | 4.8E-01 | −0.015 | |
17 | rs9912900 | 71057060 | −5.17 | 2.7E-07 | 0.044 | −0.276 | 0.69 | 7.5E-01 | 0.175 | SLC39A11 |
17 | rs2589133 | 78793476 | −5.05 | 5.1E-07 | 0.071 | −0.296 | −1.52 | 6.8E-02 | −0.386 | RPTOR |
Note: “Chr.” is chromosome. Position is for reference genome build hg19/GRCh37. Signs of the T statistics (T) give the direction of effect in the MWAS and replication, respectively, where a negative value indicates a decreased methylation level in the SZ cases. Effect is effects size calculated by Cohen’s d (mean difference between the cases and controls divided by a pooled estimate of the standard deviation) is calculated for the replication sample only. Gene is name of the gene allowing for a ±20 Kb flanking region. CpG-SNPs in bold reach significance in the replication after a Bonferroni correction for multiple testing.