Table 3.
Significant schizophrenia-associated differentially methylated regions (DMRs). Shown in chromosomal order is the location of significant (Šidák-corrected P < 0.05) DMRs identified in each of the four brain regions, with the median P-value for DMR probes given for the other three brain regions (bold denotes median P < 0.05 and grey boxes denote regions that were not identified in that brain region). The ‘Gene’ column lists the combined Illumina and Genomic Regions Enrichment of Annotation Tool (GREAT) annotation (38).
| Region | Gene(s) | Probes | N probes | Prefrontal cortex |
Striatum |
Hippocampus |
Cerebellum |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Median P | Šidák P | Median P | Šidák P | Median P | Šidák P | Median P | Šidák P | ||||
| chr1:25257505-25257814 | RUNX3 | cg07996594; cg04221877; cg15014975; cg24019564; cg10993442; cg24842859; cg20695936; cg13106389; cg18087266; cg25882256; cg04250451; cg10013501 | 12 | 1.22E-02 | 1.02E-02 | 0.36 | 0.66 | 0.29 | |||
| chr1:89664260-89664583 | GBP4 | cg23978657; cg02482460; cg22221320; cg21365602; cg20410995; cg14563196 | 6 | 8.36E-03 | 5.36E-04 | 3.16E-12 | 0.93 | 7.06E-02 | |||
| chr1:160336475-160336713 | NHLH1 | cg18023842; cg08247612; cg13992678; cg00006397; cg00881010 | 5 | 0.24 | 0.62 | 0.42 | 8.00E-04 | 1.64E-05 | |||
| chr1:175162044-175162398 | KIAA0040; TNN; TNR | cg11908570; cg22626041; cg26563583; cg17839543; cg18880390; cg00099768; cg13857382; cg11973900; cg08873628; cg00321850 | 10 | 2.34E-02 | 7.62E-04 | 0.47 | 0.25 | 0.25 | |||
| chr2:241936844-241937035 | SNED1 | cg16937168; cg03785076; cg21304158 | 3 | 0.45 | 0.74 | 0.89 | 5.16E-05 | 6.68E-05 | |||
| chr4:1202653-1202967 | LOC100130872- SPON2; CTBP1 | cg14527262; cg04228083; cg17227257; cg16721321; cg26130533; cg14505741; cg11104416; cg18085660; cg11888738; cg01638225; cg21082272 | 11 | 3.61E-02 | 1.32E-02 | 0.41 | 0.66 | 0.72 | |||
| chr4:2627014-2627247 | FAM193A; TNIP2; RNF4 | cg25790133; cg05083414; cg05949640; cg22980079; cg14549256; cg20163033; cg00097088 | 7 | 7.22E-03 | 2.93E-02 | 0.56 | 0.94 | 0.44 | |||
| chr5:23506738-23507031 | PRDM9 | cg04362002; cg10589310 | 2 | 5.91E-02 | 3.76E-02 | 0.11 | 4.69E-06 | 3.65E-05 | |||
| chr5:23507450-23507657 | cg22054885; cg19837938; cg02444433; cg25472530; cg22079902; cg01667892 | 6 | 0.10 | 0.11 | 0.45 | 5.33E-04 | 5.49E-08 | ||||
| chr6:30853948-30854234 | DDR1 | cg16215084; cg25251478; cg26321999; cg00934322; cg07187855; cg24566261; cg09965419; cg17091577 | 8 | 2.28E-02 | 7.87E-03 | 0.75 | 0.73 | 0.21 | |||
| chr7:5535463-5535935 | MIR589; TNRC18; FBXL18 | cg01942816; cg22108567; cg25343388; cg09286367; cg17419731; cg01024247; cg00966405; cg04155485 | 8 | 5.48E-03 | 3.44E-03 | 0.55 | 0.36 | 0.54 | |||
| chr8:145728203-145728631 | GPT | cg16587265; cg14476479; cg23793500; cg00280345; cg16582889; cg07658280; cg26572973; cg05241828; cg09957864; cg25600446; cg06110286; cg19352605 | 12 | 1.80E-03 | 5.53E-09 | 0.49 | 0.74 | 0.51 | |||
| chr10:124638756-124639111 | FAM24B; LOC399815 | cg03804621; cg16299003; cg11218091; cg14708218; cg18195080; cg15252215 | 6 | 1.05E-02 | 4.88E-03 | 0.47 | 5.15E-03 | 4.71E-04 | |||
| chr10:131264786-131265074 | MGMT | cg26950715; cg02330106; cg12575438; cg02022136; cg23998405; cg01341123; cg25946389 | 7 | 0.13 | 0.54 | 0.83 | 1.01E-02 | 7.35E-03 | |||
| chr11:192897-193063 | ODF3; SCGB1C1; LOC653486 | cg18793661; cg22280333; cg03960562; cg02378673; cg20297976 | 5 | 0.26 | 0.62 | 0.25 | 4.55E-04 | 2.08E-05 | |||
| chr11:34460298-34460558 | CAT | cg20731136; cg06027906; cg07768201; cg03720043; cg02109652; cg06908474; cg01847719 | 7 | 0.36 | 3.61E-02 | 1.00E-02 | 9.44E-04 | 0.21 | |||
| chr12:125145446-125145642 | NCOR2; SCARB1 | cg12077664; cg27645498; cg19888509 | 3 | 2.00E-03 | 2.20E-02 | 0.56 | 0.59 | 0.18 | |||
| chr12:131452238-131452298 | SFSWAP; GPR133 | cg24336338; cg03776878; cg23617848 | 3 | 0.80 | 0.23 | 0.59 | 1.20E-04 | 2.50E-03 | |||
| chr13:114202683-114202862 | TFDP1; TMCO3 | cg16567723; cg24121069; cg11312353 | 3 | 6.38E-04 | 1.94E-02 | 0.12 | 0.74 | 9.18E-03 | |||
| chr16:2892518-2892913 | PRSS30P; TMPRSS8 | cg07645761; cg00491180; cg01006802; cg27137258; cg10448227; cg10186456 | 6 | 7.18E-03 | 5.65E-03 | 3.91E-02 | 0.12 | 4.27E-03 | 1.62E-04 | ||
| chr17:154410-154672 | DOC2B; RPH3AL | cg08770870; cg11940040; cg10440639; cg23246911 | 4 | 8.27E-04 | 1.02E-04 | 7.14E-03 | 1.78E-02 | 3.86E-03 | 3.44E-02 | ||
| chr19:19639970-19640076 | YJEFN3 | cg11244672; cg20098710 | 2 | 3.00E-04 | 4.49E-02 | 0.43 | 0.50 | 0.54 | |||
| chr19:57742112-57742445 | AURKC | cg25802888; cg19568003; cg18644286; cg26332114; cg19603903; cg23371413; cg06643849; cg25432232; cg22711741 | 9 | 0.23 | 1.34E-02 | 2.64E-03 | 0.86 | 0.27 | |||
| chr21:46898048-46898138 | COL18A1; SLC19A1 | cg03208198; cg20383948 | 2 | 1.30E-04 | 2.31E-02 | 0.68 | 0.49 | 0.14 | |||