Table 2. TWAS genes with association to schizophrenia and chromatin phenotypes.
42 genes (including 7 genes at novel loci, highlighted with a [*]) had a significant TWAS association with SCZ and chromatin phenotypes. For each significant TWAS association with SCZ, the number of significant genechromatin associations (FWER 5% among TWAS gene-mark associations, by Bonforroni correction) are reported. In the middle columns ‘.’ represents genes that were not heritable in the study and therefore not TWAS-associated. In the right columns ‘.’ represents no identified association; genes with no chromatin associations are not shown. Top panel shows results from genes, with TSS listed as position; bottom panel shows results from splicing events in CMC with exon-exon junction listed as position (details in Supplementary Table 18). The minority of loci without subsequent evidence of colocalziation of molecular phenotype with SCZ are indicated with † (see Supplementary Table 3 for full numerical results).
| Gene | Chr | Position | TWAS P-value
|
Associated marks
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| YFS/blood | MET/adipose | NTR/blood | CMC/brain | DHS | H3K27AC | H3K4ME1 | H3K4ME3 | PU1 | RPB2 | |||
| RERE | 1 | 8,483,747 | 4e-07 | 2e-06 | 2e-06 | . | . | . | . | . | . | 3 |
| SLC45A1 | 1 | 8,378,144 | . | . | . | 4e-08 | . | . | . | . | . | 1 |
| MAP7D1* | 1 | 36,621,565 | 6e-04 | . | 1e-06 | . | . | . | . | . | . | 1 |
| MED8 | 1 | 43,855,483 | 5e-01 | . | . | 2e-06 | . | . | 1 | . | . | . |
| ANP32E | 1 | 150,207,026 | . | . | 1e-08 | . | . | . | . | 1 | . | . |
| MRPS21 | 1 | 150,266,261 | 3e-06 | 3e-03 | 6e-03 | 2e-02 | . | . | 1 | . | . | . |
| RFWD2*† | 1 | 176,176,380 | 4e-06 | . | . | . | . | . | 1 | . | . | . |
| C2orf69 | 2 | 200,775,978 | . | 6e-10 | . | . | . | . | . | 1 | . | . |
| GLT8D1† | 3 | 52,737,714 | . | . | 5e-08 | 3e-08 | . | 1 | . | . | . | . |
| GLYCTK | 3 | 52,321,835 | 2e-08 | . | . | . | . | 1 | . | . | . | . |
| GNL3 | 3 | 52,719,935 | 7e-09 | 6e-07 | . | 5e-02 | . | . | . | 1 | . | . |
| NEK4† | 3 | 52,804,965 | . | . | . | 2e-09 | . | . | . | 1 | . | . |
| NT5DC2† | 3 | 52,567,793 | 6e-06 | 6e-06 | . | 7e-01 | . | 1 | . | 1 | . | . |
| PPM1M | 3 | 52,279,808 | 2e-07 | 2e-07 | . | 2e-03 | . | 1 | . | . | . | . |
| TMEM110 | 3 | 52,931,597 | 1e-02 | 4e-01 | 1e-08 | 6e-06 | . | 1 | 1 | 2 | . | . |
| PCCB | 3 | 135,969,166 | 1e-08 | 1e-10 | . | 3e-10 | 1 | . | 3 | . | . | . |
| RP11-53O19.3 | 5 | 44,826,178 | . | 6e-06 | . | . | . | . | 1 | . | . | . |
| DND1 | 5 | 140,053,171 | . | 8e-07 | 1e-02 | . | . | 1 | . | 1 | . | . |
| IK† | 5 | 140,027,383 | 4e-06 | 1e-06 | . | 5e-05 | . | 1 | . | 1 | . | . |
| NDUFA2 | 5 | 140,027,370 | 2e-06 | . | . | 4e-06 | . | 1 | . | 2 | . | . |
| PCDHA2 | 5 | 140,174,443 | . | . | . | 7e-06 | . | 1 | . | 1 | . | . |
| ZMAT2 | 5 | 140,080,031 | 5e-06 | 1e-03 | . | 3e-06 | . | . | . | 1 | . | . |
| AS3MT | 10 | 104,629,209 | . | 6e-08 | 7e-09 | 1e-05 | . | 1 | . | . | . | . |
| MPHOSPH9† | 12 | 123,717,785 | 4e-09 | 1e-05 | . | 2e-08 | . | 1 | . | . | 1 | . |
| KIAA0391* | 14 | 35,591,526 | 7e-01 | 2e-07 | 5e-01 | . | . | 2 | 1 | . | . | . |
| PPP2R3C* | 14 | 35,591,748 | 6e-05 | 1e-01 | 3e-06 | 2e-02 | . | 2 | 2 | . | . | . |
| MAPK3 | 16 | 30,134,630 | 5e-05 | . | . | 1e-06 | . | 1 | . | . | . | 1 |
| GFOD2 | 16 | 67,753,273 | . | . | 6e-07 | 2e-05 | . | 1 | . | 2 | . | . |
| TSNAXIP1 | 16 | 67,840,780 | . | . | . | 2e-06 | . | . | 1 | 2 | . | . |
| DUS2L | 16 | 68,038,024 | 1e-06 | . | 3e-06 | 4e-04 | . | . | . | 2 | . | . |
| PRMT7† | 16 | 68,344,876 | 1e-05 | 8e-04 | . | 8e-06 | . | . | 1 | 1 | . | . |
| GRAP* | 17 | 18,950,336 | . | . | 5e-07 | . | . | . | . | . | . | 1 |
| RNF112* | 17 | 19,314,490 | 8e-06 | . | . | . | . | . | . | . | . | 1 |
| ACTR5† | 20 | 37,377,096 | 2e-07 | 2e-04 | . | 7e-01 | 1 | . | 1 | . | . | . |
| CBR3 | 21 | 37,507,262 | 6e-03 | 2e-03 | 2e-06 | 5e-04 | 1 | . | 2 | . | . | . |
|
| ||||||||||||
| CMC/brain splicing | ||||||||||||
| TBC1D5 | 3 | 17,255,862 - 17,279,655 | . | . | . | 3e-06 | . | . | 1 | . | . | . |
| NEK4† | 3 | 52,800,010 - 52,800,194 | . | . | . | 1e-06 | . | . | 1 | . | . | . |
| CCDC90B | 11 | 82,985,783 - 82,991,184 | . | . | . | 3e-07 | . | 1 | . | . | . | . |
| SBNO1† | 12 | 123,821,038 - 123,825,535 | . | . | . | 4e-10 | . | . | . | . | 1 | . |
| KLC1 | 14 | 104,145,855 - 104,151,323 | . | . | . | 7e-12 | . | . | 1 | 1 | . | . |
| RTN1* | 14 | 60,074,210 - 60,193,637 | . | . | . | 1e-06 | . | . | 1 | . | . | . |
| TAOK2† | 16 | 29,997,825 - 29,998,165 | . | . | . | 4e-06 | . | . | . | . | . | †1 |
| PPP4C† | 16 | 30,094,168 - 30,094,715 | . | . | . | 2e-06 | . | . | . | . | . | †1 |
Novel, not overlapping 108 PGC SCZ GWAS loci.
No significant SCZ colocalization posterior in any reference (exlucding chromatin features in YRI).