Table 2.
The SNPs with suggestive signal associated with age at onset of schizophrenia between different comparisons
| Chr | SNP | Position | Gene | GWAS probands of extreme contrast in the AAO (n = 185) | Co-affected siblings of extreme contrast in the AAO (n = 181) | Trend of the AAO among 4 groups of probands§ (n = 475) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ALm | MAFE | MAFL | ORa | P-value | Empirical P-value | MAFE | MAFL | ORa | P-value | ORb | P-value | ||||
| 1 | rs12118952 | 81,445,881 | ADGRL2 | A | 0.25 | 0.46 | 0.38 | 3.8 × 10−5 | 1.6 × 10−5 | 0.30 | 0.40 | 0.66 | 0.06 | 0.66 | 8.9 × 10−4 |
| 1 | rs6426994 | 166,361,616 | FMO7P | G | 0.30 | 0.49 | 0.39 | 9.6 × 10−5 | 5.5 × 10−5 | — | — | — | — | — | — |
| 1 | rs609832 | 211,552,050 | RD3/SLC30A1 | G | 0.18 | 0.04 | 6.32 | 3.6 × 10−5 | 5.3 × 10−6 | 0.14 | 0.07 | 2.44 | 0.02 | 1.95 | 8.9 × 10−4 |
| 1 | rs2378013 | 218,778,121 | TGFB2 | A | 0.41 | 0.20 | 2.68 | 7.5 × 10−5 | 3.6 × 10−5 | 0.33 | 0.26 | 1.44 | 0.13 | 1.62 | 5.9 × 10−4 |
| 4 | rs923673 | 20,789,574 | KCNIP4 | C | 0.30 | 0.12 | 4.08 | 1.3 × 10−5 | 3.2 × 10−6 | 0.25 | 0.17 | 1.69 | 0.06 | 1.69 | 3.4 × 10−4 |
| 4 | rs11930588 | 40,179,089 | N4BP2 | T | 0.49 | 0.30 | 3.02 | 5.1 × 10−5 | 1.6 × 10−5 | 0.43 | 0.36 | 1.41 | 0.14 | 1.46 | 1.7 × 10−4 |
| 6 | rs2506754 | 103,548,429 | R3HDM2P2 | A | 0.30 | 0.12 | 3.94 | 1.2 × 10−5 | 1.9 × 10−6 | 0.22 | 0.18 | 1.37 | 0.25 | 1.88 | 2.6 × 10−3 |
| 6 | rs12210422 | 103,595,851 | R3HDM2P2 | G | 0.35 | 0.15 | 3.01 | 8.9 × 10−5 | 3.8 × 10−5 | 0.30 | 0.25 | 1.31 | 0.26 | 1.64 | 5.5 × 10−6 |
| 6 | rs6900852 | 125,901,926 | NCOA7 | G | 0.37 | 0.43 | 0.39 | 9.8 × 10−5 | 5.2 × 10−5 | 0.42 | 0.49 | 0.73 | 0.14 | 0.62 | 1.0 × 10−4 |
| 6 | rs3016537 | 161,816,611 | PARK2 | C | 0.13 | 0.30 | 0.27 | 4.1 × 10−5 | 1.6 × 10−5 | — | — | — | — | — | — |
| 6 | rs7755434 | 161,816,624 | PARK2 | A | 0.12 | 0.29 | 0.26 | 2.7 × 10−5 | 9.6 × 10−6 | — | — | — | — | — | — |
| 6 | rs60117510 | 161,816,881 | PARK2 | C | 0.12 | 0.29 | 0.25 | 2.2 × 10−5 | 9.1 × 10−6 | 0.12 | 0.26 | 0.40 | 0.001 | 0.64 | 2.5 × 10−3 |
| 7 | rs6964070 | 4,463,521 | SDK1/FOXK1 | G | 0.53 | 0.35 | 2.63 | 9.3 × 10−5 | 4.5 × 10−5 | 0.49 | 0.36 | 1.73 | 0.01 | 1.51 | 1.1 × 10−3 |
| 7 | rs1589988 | 16,227,085 | ISPD | A | 0.18 | 0.34 | 0.34 | 7.6 × 10−5 | 2.9 × 10−5 | 0.20 | 0.31 | 0.55 | 0.02 | 0.62 | 4.0 × 10−4 |
| 18 | rs571002 | 13,090,667 | CEP192 | T | 0.22 | 0.42 | 0.33 | 7.7 × 10−5 | 3.8 × 10−5 | 0.29 | 0.36 | 0.73 | 0.17 | 0.61 | 1.5 × 10−4 |
| 19 | rs371164 | 6,489,802 | DENND1C/TUBB4A | G | 0.53 | 0.40 | 2.52 | 6.3 × 10−5 | 2.9 × 10−5 | 0.49 | 0.34 | 1.98 | 0.004 | 1.53 | 4.2 × 10−4 |
| 21 | rs2830964 | 27,474,617 | RPL10P1/NCSTNP1 | C | 0.22 | 0.39 | 0.34 | 8.4 × 10−5 | 3.8 × 10−5 | 0.27 | 0.32 | 0.72 | 0.19 | 0.65 | 8.0 × 10−4 |
Chr: chromosome; bold: SNP within the gene; italics: SNP near the gene; ALm: minor allele; AAO: age at onset; MAFE/MAFL: minor allele frequency in patients from families with earliest/latest AAO; ORa: odds ratio from association test using logistic regression; ORb: odds ratio from trend test using ordinal logistic regression. Empirical P presented the P-values obtained after up to 108 times of permutation of the multiple logistic model. §The trend effect of each SNP was tested using ordinal logistic regression among 4 groups of probands from families with earliest, earlier, later, and latest AAO of schizophrenia.