Table 3.
Additional analyses of individual genotyping data for 10 top-performing SNPs selected for mathematics ‘SNP set'
| SNP rsID | Chr | Position | Allele | N | Additive model F | Additive model P | Genotypic model F | Genotypic model P | Non- additivity F | Non- additivity P | Case- control P | OR (CI) | Nearest gene |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs11225308 | 11 | 101904688 | G | 2179 | 12.78 | 0.0002 | 7.43 | 0.0003 | 2.07 | 0.1502 | 0.0001 | 1.43 (1.12–1.82) | MMP7 |
| rs363449 | 21 | 29906146 | C | 2177 | 10.63 | 0.0006 | 5.43 | 0.0022 | 0.24 | 0.6231 | 0.0017 | 1.50 (1.03–2.25) | GRIK1 |
| Rs17278234 | 5 | 13990476 | C | 2183 | 9.99 | 0.0008 | 5.05 | 0.0032 | 0.11 | 0.7395 | 0.0437 | 1.20 (0.94–1.53) | DNAH5 |
| Rs11154532 | 6 | 130567068 | C | 2173 | 6.51 | 0.0054 | 3.45 | 0.0159 | 0.40 | 0.5264 | 0.0005 | 1.42 (1.11–1.81) | SAMD3 |
| Rs12199332 | 6 | 157185419 | A | 2111 | 5.69 | 0.0086 | 4.13 | 0.0081 | 2.57 | 0.1094 | 0.2563 | 1.13 (0.88–1.46) | ARID1B |
| Rs12613365 | 2 | 191055555 | G | 2179 | 3.87 | 0.0246 | 1.95 | 0.0713 | 0.03 | 0.8640 | 0.2427 | 1.10 (0.67–1.89) | FLJ20160 |
| Rs6588923 | 11 | 106125102 | A | 2111 | 3.78 | 0.0260 | 2.14 | 0.0590 | 0.50 | 0.4802 | 0.0663 | 1.26 (0.94–1.66) | GUCY1A2 |
| Rs2300052 | 7 | 107875730 | G | 2109 | 3.04 | 0.0407 | 1.60 | 0.1011 | 0.16 | 0.6887 | 0.0863 | 1.42 (0.88–2.40) | NRCAM |
| Rs6947045 | 7 | 107287183 | C | 2179 | 2.87 | 0.0451 | 2.70 | 0.0338 | 2.52 | 0.1128 | 0.1803 | 0.96 (0.70–1.33) | DLD |
| Rs1215603 | 12 | 105041007 | C | 2179 | 2.83 | 0.0463 | 1.42 | 0.1212 | 0.01 | 0.9358 | 0.0543 | 1.25 (0.91–1.74) | NUAK1 |
The table is ordered by additive model P-value (one-tailed). The first three SNP associations survive Bonferroni correction for multiple testing. SNP rsID, dbSNP rsID; Chr, chromosome; Position, physical position; Allele, allele associated with lower mathematical ability in our sample; N, Sample N; Additive model F, F-statistic from the additive model on 1 and N− 2 degrees of freedom; Additive model P = one-tailed P value from additive model; % Variance = variance in mathematical ability explained by the additive model; Genotypic model F = F-statistic from the genotypic model on 1 and N − 3 degrees of freedom; Genotypic model P, one-tailed P-value from genotypic model; Non-additivity F, F-statistic from the additive vs. genotypic model comparison on 1 degree of freedom; Non-additivity P, P-value from likelihood ratio test comparison of additive and genotypic models; Case-control P = one -tailed P-value from logistic regression test (with 1 degree of freedom) of association with case status defined as the lowest-performing 15%; OR (CI), Odds ratio for case risk; Nearest gene, Nearest gene annotation from NetAffx (http://www.affymetrix.com/analysis/index.affx).