Table 3.
20 SNPs with the Smallest p Values with Each of the Nine Factors as Quantitative Traits
| SNP Name | Position (Build 35) | Gene/Locus |
Trios |
Cases |
Combined |
Factor Responsible for the p Value | |||
|---|---|---|---|---|---|---|---|---|---|
| p Value | Effect Sizea | p Value | Effect Sizea | p Value | Effect Sizea | ||||
| rs2019080 | 79951742 | 3.92 × 10−2 | 0.25 (0.00–0.50) | 1.23 × 10−2 | 0.17 (0.03–0.31) | 8.24 × 10−4 | 0.28 (0.11–0.44) | delusion | |
| rs1574190 | 80662387 | RAI17 | 1.04 × 10−3 | 0.43 (0.14–0.72) | 7.02 × 10−4 | 0.24 (0.10–0.39) | 2.02 × 10−4 | 0.33 (0.14–0.51) | prodromal |
| rs4319456 | 82927110 | ∗ | 1.11 × 10−2 | 0.50 (0.09–0.92) | 1.31 × 10−3 | 0.35 (0.13–0.57) | 5.79 × 10−4 | 0.46 (0.20–0.71) | disorganization |
| rs7899151 | 82938902 | ∗ | 1.62 × 10−3 | 0.67 (0.22–1.12) | 2.01 × 10−3 | 0.34 (0.10–0.57) | 4.27 × 10−4 | 0.48 (0.20–0.76) | disorganization |
| rs10883866 | 83633619 | NRG3 | 7.26 × 10−7 | 0.97 (0.49–1.45) | 5.27 × 10−6 | 0.51 (0.28–0.74) | 2.30 × 10−7 | 0.67 (0.37–0.97) | delusion |
| rs10748842 | 83639719 | NRG3 | 7.26 × 10−7 | 0.97 (0.49–1.45) | 5.27 × 10−6 | 0.51 (0.28–0.74) | 2.30 × 10−7 | 0.67 (0.37–0.97) | delusion |
| rs6584400 | 83646506 | NRG3 | 8.40 × 10−6 | 0.75 (0.36–1.14) | 1.51 × 10−5 | 0.44 (0.24–0.64) | 1.59 × 10−6 | 0.55 (0.30–0.81) | delusion |
| rs17099528 | 83921863 | NRG3 | 5.72 × 10−3 | 67.2 (−4.8–139) | 2.94 × 10−3 | 1.90 (0.46–3.33) | 1.34 × 10−3 | 2.53 (0.85–4.22) | disorganization |
| rs951204 | 84038745 | NRG3 | 5.46 × 10−3 | 0.47 (0.12–0.83) | 1.60 × 10−2 | 0.23 (0.03–0.43) | 1.24 × 10−3 | 0.37 (0.13–0.61) | disorganization |
| rs12416489 | 84717603 | NRG3 | 4.73 × 10−2 | 0.22 (0.00–0.44) | 3.78 × 10−2 | 0.14 (0.00–0.27) | 1.24 × 10−3 | 0.25 (0.09–0.41) | scholastic |
| rs11196700 | 84724720 | NRG3 | 6.01 × 10−3 | 0.32 (0.09–0.54) | 1.24 × 10−2 | 0.17 (0.03–0.31) | 3.42 × 10−4 | 0.29 (0.12–0.46) | scholastic |
| rs3818306 | 84728393 | NRG3 | 4.73 × 10−2 | 0.22 (0.00–0.44) | 3.78 × 10−2 | 0.14 (0.00–0.27) | 1.24 × 10−3 | 0.25 (0.09–0.41) | scholastic |
| rs8421 | 84736601 | NRG3b | 6.01 × 10−3 | 0.32 (0.09–0.54) | 1.20 × 10−2 | 0.17 (0.03–0.31) | 3.36 × 10−4 | 0.29 (0.12–0.45) | scholastic |
| rs1339844 | 84856649 | NRG3b | 3.76 × 10−3 | 0.36 (0.09–0.64) | 3.15 × 10−2 | 0.16 (0.01–0.30) | 2.74 × 10−4 | 0.32 (0.14–0.49) | scholastic |
| rs10886221 | 85123936 | ∗ | 1.12 × 10−1 | 0.22 (−0.06–0.50) | 7.48 × 10−2 | 0.13 (−0.02–0.29) | 8.94 × 10−4 | 0.30 (0.12–0.47) | hallucination |
| rs12220927 | 89980527 | 6.04 × 10−2 | 0.28 (0.01–0.56) | 8.00 × 10−3 | 0.23 (0.07–0.38) | 1.45 × 10−4 | 0.40 (0.19–0.60) | disability/impairment | |
| rs4934396 | 90108138 | C10orf59 | 1.09 × 10−2 | 0.61 (0.05–1.18) | 6.64 × 10−3 | 0.33 (0.07–0.59) | 8.50 × 10−4 | 0.50 (0.18–0.82) | disorganization |
| rs11202748 | 90199318 | C10orf59 | 5.50 × 10−3 | 0.42 (0.10–0.74) | 2.24 × 10−2 | 0.19 (0.02–0.36) | 2.76 × 10−4 | 0.37 (0.16–0.58) | disorganization |
| rs10509546 | 90201633 | C10orf59 | 4.25 × 10−3 | 0.53 (0.14–0.92) | 2.13 × 10−2 | 0.23 (0.03–0.43) | 5.77 × 10−4 | 0.42 (0.17–0.67) | disorganization |
| rs10430719 | 91028961 | 4.75 × 10−2 | 0.32 (0.00–0.63) | 2.27 × 10−2 | 0.19 (0.01–0.37) | 3.33 × 10−4 | 0.37 (0.14–0.60) | prodromal | |
a
AddVal values from the UNPHASED output results. For quantitative traits, this value shows the estimated additive genetic value for this risk allele compared to the nonrisk allele, assuming a normally distributed trait and small deviations from the mean.
b
3′ downstream of NRG3, which is within the LD block containing the last 5 exons of NRG3.
∗
Located in the gene deserts flanking NRG3.