Table 3.
The significant and novel genes overlapping with no known GWAS risk variants within ±500 kb as identified by aSPU applied to the SCZ2 data. The validated gene-trait associations appeared in the following references: [1] Goes et al. (2015); [2] Schizophrenia Working Group (2014).
| Weight | Gene | CHR | P0 | P1 | aSPU | TWAS | SSU | Most sig. SNP | Validation |
|---|---|---|---|---|---|---|---|---|---|
| YFS/NTR | MAP7D1 | 1 | 36621801 | 36646448 | 5.0E-07 | 5.2E-07 | 6.7E-07 | 3.3E-07 | |
| YFS | CNN3 | 1 | 95362507 | 95392834 | 9.0E-07 | 7.1E-02 | 7.4E-08 | 9.4E-07 | |
| CMC-introns | GABPB2 | 1 | 151043079 | 151091007 | 7.0E-07 | 4.5E-07 | 4.5E-07 | 5.6E-08 | |
| CMC-introns | TBC1D5 | 3 | 17198653 | 17784240 | 1.7E-06 | 3.1E-06 | 1.7E-06 | 5.5E-08 | [1] |
| YFS | IK | 5 | 140026643 | 140042064 | 1.4E-06 | 6.4E-07 | 4.3E-07 | 3.6E-07 | |
| CMC-introns | CXXC5 | 5 | 139028300 | 139062680 | 1.0E-07 | 2.1E-09 | 1.9E-08 | 1.5E-06 | |
| YFS | TMCO6 | 5 | 140019012 | 140024993 | 1.8E-06 | 1.1E-04 | 4.2E-07 | 3.6E-07 | |
| METSIM | DND1 | 5 | 140050379 | 140053171 | 8.0E-07 | 3.6E-06 | 1.1E-06 | 3.6E-07 | |
| CMC | ZMAT2 | 5 | 140080031 | 140086239 | 1.5E-06 | 1.6E-05 | 1.9E-07 | 3.6E-07 | |
| YFS | ABCB1 | 7 | 87133175 | 87342611 | 1.8E-06 | 5.5E-04 | 2.5E-07 | 1.4E-07 | [1] |
| METSIM/CMC-introns | ZDHHC2 | 8 | 17013538 | 17082308 | 2.0E-07 | 5.0E-06 | 7.3E-08 | 1.1E-07 | [1] |
| CMC-introns | FGFR1 | 8 | 38268655 | 38326352 | 3.0E-07 | 8.5E-07 | 7.6E-07 | 2.3E-07 | |
| YFS | ENDOG | 9 | 131580753 | 131584956 | 1.2E-06 | 6.4E-07 | 9.2E-07 | 1.9E-06 | |
| METSIM | PKN3 | 9 | 131464802 | 131483197 | 6.0E-07 | 8.2E-01 | 2.2E-08 | 1.9E-06 | |
| CMC | TEK | 9 | 27109146 | 27230172 | 4.0E-07 | 1.1E-07 | 6.4E-08 | 4.7E-07 | [1] |
| YFS | ZDHHC5 | 11 | 57435219 | 57468659 | 2.0E-07 | 2.2E-07 | 1.2E-07 | 6.7E-08 | [2] |
| NTR/METSIM | CLIP1 | 12 | 122755979 | 122907179 | 1.7E-06 | 1.9E-04 | 9.2E-08 | 3.8E-06 | [1] |
| CMC | CCDC92 | 12 | 124420954 | 124457163 | 1.0E-06 | 6.8E-03 | 6.5E-06 | 4.1E-07 | |
| YFS/NTR | PPP2R3C | 14 | 35554678 | 35591519 | 6.0E-07 | 2.7E-07 | 3.2E-07 | 1.5E-07 | |
| METSIM | KIAA0391 | 14 | 35591052 | 35743271 | 5.0E-07 | 6.6E-07 | 3.0E-07 | 1.5E-07 | [1] |
| METSIM | PCNX | 14 | 71374122 | 71582099 | 1.0E-06 | 3.8E-06 | 1.8E-07 | 1.6E-07 | [1] |
| CMC-introns | AP3B2 | 15 | 83328032 | 83378635 | 1.0E-07 | 1.7E-06 | 8.5E-08 | 5.5E-08 | |
| METSIM/CMC-introns | NMRAL1 | 16 | 4511694 | 4524896 | 5.0E-07 | 1.6E-07 | 9.3E-06 | 2.8E-07 | |
| CMC | CORO7 | 16 | 4404542 | 4466962 | 6.0E-07 | 5.2E-07 | 4.8E-07 | 2.8E-07 | |
| CMC | CPNE7 | 16 | 89642175 | 89663654 | 1.0E-07 | 5.0E-08 | 4.4E-07 | 1.1E-07 | |
| YFS/CMC | CHMP1A | 16 | 89710838 | 89724193 | 1.4E-06 | 1.5E-02 | 9.1E-08 | 1.1E-07 | |
| CMC-introns | TCF25 | 16 | 89939993 | 89977792 | 5.0E-07 | 1.4E-02 | 6.8E-08 | 1.1E-07 | |
| CMC-introns | CDK10 | 16 | 89753075 | 89762772 | 1.7E-06 | 2.1E-01 | 9.4E-08 | 1.1E-07 | |
| CMC | RPL13 | 16 | 89627064 | 89633237 | 1.5E-06 | 7.8E-04 | 1.6E-07 | 1.1E-07 | |
| YFS | PRPSAP2 | 17 | 18743398 | 18834581 | 1.0E-07 | 5.6E-08 | 5.3E-07 | 7.8E-07 | |
| METSIM | KCNG2 | 18 | 77623668 | 77660184 | 1.9E-06 | 4.5E-03 | 5.1E-08 | 2.2E-07 | [1] |
| CMC | SNRNP70 | 19 | 49588464 | 49611870 | 1.0E-07 | 2.1E-03 | 1.7E-08 | 2.2E-07 |