Table 2.
Top results from the GWASs
| Test | Trait | Marker ID | Chromosome | Position | MAF | Gene (protein coding) | Effect allele | Other allele | Probands | Effect | SE | χ2 | p-value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| General | WISC Arithmetic | psy_rs7826548 | 8 | 2955158 | 0.4717 | CSMD1 | C | T | 389 | − 0.199 | 0.036 | 31.12 | 2 × 10–8 |
| General | WISC Arithmetic | rs2554728 | 8 | 3842999 | 0.2731 | CSMD1 | T | C | 396 | − 0.155 | 0.028 | 30.47 | 3 × 10–8 |
| General | WISC Arithmetic | rs11995240 | 8 | 3848025 | 0.1691 | CSMD1 | T | C | 396 | − 0.016 | 0.003 | 29.84 | 5 × 10–8 |
| General | WISC Arithmetic | rs17068473 | 8 | 3854987 | 0.2854 | CSMD1 | G | T | 396 | 0.183 | 0.033 | 30.72 | 3 × 10–8 |
| General | WISC Arithmetic | rs4875262 | 8 | 3876265 | 0.3858 | CSMD1 | G | A | 396 | 0.262 | 0.046 | 31.95 | 2 × 10–8 |
| General | WISC Arithmetic | rs2740929 | 8 | 3879918 | 0.4877 | CSMD1 | C | T | 396 | − 0.191 | 0.034 | 31.03 | 3 × 10–8 |
| General | WISC Arithmetic | rs2740878 | 8 | 3918118 | 0.3288 | CSMD1 | A | G | 396 | − 0.309 | 0.054 | 33.05 | 9 × 10–9 |
| General | WISC Arithmetic | rs2552166 | 8 | 3920395 | 0.1734 | CSMD1 | G | A | 396 | − 0.326 | 0.057 | 32.16 | 1 × 10–8 |
| General | WISC Arithmetic | rs6049002 | 20 | 296172 | 0.3721 | C | T | 398 | 0.132 | 0.024 | 30.56 | 3 × 10–8 | |
| General | WISC Arithmetic | rs6117457 | 20 | 733963 | 0.2883 | T | C | 398 | − 0.359 | 0.062 | 33.9 | 6 × 10–9 | |
| General | WISC Arithmetic | psy_rs79359757 | 20 | 937853 | 0.07381 | C | T | 398 | − 0.053 | 0.01 | 30.01 | 4 × 10–8 | |
| General | WISC Arithmetic | rs7261002 | 20 | 1002656 | 0.1835 | G | A | 398 | 0.366 | 0.064 | 32.9 | 1 × 10–8 | |
| General | WISC Arithmetic | rs6118727 | 20 | 1030235 | 0.4465 | A | G | 398 | 0.071 | 0.013 | 30.15 | 4 × 10–8 | |
| General | WISC Arithmetic | rs200896 | 20 | 1789409 | 0.4292 | A | C | 398 | − 0.326 | 0.056 | 33.38 | 8 × 10–9 | |
| General | WISC Arithmetic | psy_rs200888 | 20 | 1796461 | 0.3931 | G | T | 396 | 0.138 | 0.025 | 30.49 | 3 × 10–8 | |
| General | WISC Arithmetic | psy_rs4813309 | 20 | 1880550 | 0.1331 | SIRPA | C | T | 397 | − 0.444 | 0.078 | 32.7 | 1 × 10–8 |
| General | WISC Arithmetic | psy_rs6035018 | 20 | 1882954 | 0.19 | SIRPA | T | C | 398 | − 0.392 | 0.068 | 33.07 | 9 × 10–9 |
| General | WISC Arithmetic | exm1519370 | 20 | 1896100 | 0.3994 | SIRPA | C | T | 388 | − 0.128 | 0.023 | 30.41 | 4 × 10–8 |
| General | WISC Arithmetic | psy_rs73069290 | 20 | 1904515 | 0.06936 | SIRPA | G | T | 398 | 0.068 | 0.012 | 30.03 | 4 × 10–8 |
| General | WISC Arithmetic | rs6035139 | 20 | 1936275 | 0.06014 | G | A | 398 | − 0.905 | 0.163 | 30.94 | 3 × 10–8 | |
| General | WISC Arithmetic | rs214831 | 20 | 2321363 | 0.3967 | TGM3 | G | A | 398 | − 0.395 | 0.067 | 35.28 | 3 × 10–9 |
| General | WISC Arithmetic | rs6137776 | 20 | 2338454 | 0.2392 | T | C | 398 | 0.281 | 0.05 | 31.82 | 2 × 10–8 | |
| General | WISC Symbol Search | rs2673776 | 6 | 152522812 | 0.4429 | SYNE1 | C | A | 396 | 0.163 | 0.029 | 31.84 | 2 × 10–8 |
| General | WISC Symbol Search | exm2270431 | 6 | 152644111 | 0.4565 | SYNE1 | C | T | 396 | 0.146 | 0.026 | 31.44 | 2 × 10–8 |
| General | WISC Symbol Search | psy_rs9478324 | 6 | 152677815 | 0.05058 | SYNE1 | G | A | 396 | 0.287 | 0.052 | 30.51 | 3 × 10–8 |
| Maternal | SRS | rs1451197 | 2 | 2741446 | 0.4993 | G | A | 213 | − 4.888 | 0.872 | 31.42 | 2 × 10–8 | |
| Maternal | SRS | rs2176347 | 2 | 45968233 | 0.4473 | PRKCE | T | G | 231 | − 3.441 | 0.624 | 30.39 | 4 × 10–8 |
| Maternal | SRS | rs7604835 | 2 | 152881908 | 0.1315 | CACNB4 | G | A | 287 | − 11.482 | 1.927 | 35.51 | 3 × 10–9 |
| Maternal | SRS | psy_rs77672109 | 4 | 35576468 | 0.01662 | C | A | 304 | − 58.859 | 10.144 | 33.67 | 7 × 10–9 | |
| Maternal | SRS | rs11934637 | 4 | 92981939 | 0.0289 | T | G | 304 | − 34.434 | 5.853 | 34.61 | 4 × 10–9 | |
| Maternal | SRS | psy_rs146416593 | 5 | 60662093 | 0.01592 | ZSWIM6 | G | A | 324 | − 33.216 | 5.844 | 32.31 | 1 × 10–8 |
| Maternal | SRS | psy_rs79166730 | 5 | 175229558 | 0.01951 | CPLX2 | G | T | 321 | − 37.303 | 5.817 | 41.13 | 1 × 10–10 |
| Maternal | SRS | exm573219 | 6 | 116325108 | 0.01879 | FRK | G | A | 325 | − 58.949 | 9.981 | 34.88 | 4 × 10–9 |
| Maternal | SRS | psy_rs78989171 | 8 | 49645477 | 0.01301 | EFCAB1 | G | T | 308 | − 58.867 | 10.204 | 33.28 | 8 × 10–9 |
| Maternal | SRS | exm754630 | 9 | 74319677 | 0.01806 | TMEM2 | T | C | 322 | − 26.113 | 4.085 | 40.87 | 2 × 10–10 |
| Maternal | SRS | rs1681993 | 12 | 63338414 | 0.01084 | G | A | 324 | − 58.96 | 10.14 | 33.81 | 6 × 10–9 | |
| Maternal | SRS | rs7956933 | 12 | 63345018 | 0.01085 | A | G | 323 | − 58.964 | 10.151 | 33.74 | 6 × 10–9 | |
| Maternal | SRS | psy_rs10860381 | 12 | 99309750 | 0.01375 | ANKS1B | G | A | 305 | − 58.851 | 10.206 | 33.25 | 8 × 10–9 |
| Maternal | WISC Arithmetic | rs11784069 | 8 | 2119582 | 0.3736 | T | G | 271 | 0.341 | 0.061 | 31.1 | 2 × 10–8 | |
| Maternal | WISC Arithmetic | rs7261002 | 20 | 1002656 | 0.1835 | G | A | 314 | 0.661 | 0.116 | 32.68 | 1 × 10–8 | |
| Maternal | WISC Symbol Search | rs2256135 | 6 | 152464839 | 0.4566 | SYNE1 | G | A | 262 | 0.264 | 0.047 | 31.95 | 2 × 10–8 |
| Paternal | RIST index | exm693219 | 8 | 28929739 | 0.02746 | KIF13B | G | A | 371 | 42.012 | 7.191 | 34.13 | 5 × 10–9 |
| Paternal | SRS | exm109001 | 1 | 156314440 | 0.01517 | TSACC | T | G | 320 | − 42.257 | 7.231 | 34.15 | 5 × 10–9 |
| Paternal | SRS | psy_rs191695175 | 8 | 122841477 | 0.01016 | T | C | 326 | − 47.854 | 5.665 | 71.36 | 3 × 10–17 | |
| Paternal | SRS | rs16908233 | 11 | 21604897 | 0.01158 | A | G | 317 | − 34.271 | 5.86 | 34.2 | 5 × 10–9 | |
| Paternal | SRS | psy_rs117476444 | 13 | 113442872 | 0.02168 | ATP11A | G | A | 320 | − 33.185 | 5.847 | 32.21 | 1 × 10–8 |
| Paternal | WISC Arithmetic | rs11784069 | 8 | 2119582 | 0.3736 | T | G | 271 | − 0.273 | 0.049 | 30.71 | 3 × 10–8 | |
| Paternal | WISC Arithmetic | rs2740939 | 8 | 3872513 | 0.4899 | CSMD1 | C | A | 253 | − 0.244 | 0.044 | 30.73 | 3 × 10–8 |
Results meeting criteria (i) and (ii) (see “Materials and methods”) are shown. Results meeting criteria (iii) and (iv) are shown in boldface. MAF: minor allele frequency (in founders; does not necessarily correspond to the effect allele frequency); SE, standard error