Table 2.
Genome-wide significant variants for each measure of cognitive function, their ancestry-specific allele frequency estimate, and replication in independent samples.
| Test | Variant | chr | Position | Coded allele | Other allele | Coded allele frequency | N | Beta (se) | P-value | P-value (edu-adj) | Ancestry-specific allele frequencya | Replication P-valueb | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Amerindian | European | African | ||||||||||||
| B-SEVLT | rs113719683 | 4 | 40433446 | T | C | 0.939 | 7562 | 0.6 (0.1) | 3.70E-08 | 6.70E-08 | 0.997 | 0.926 | 1.000 | 0.800 |
| rs112178366 | 4 | 40433442 | A | G | 0.939 | 7562 | 0.6 (0.1) | 4.06E-08 | 6.81E-08 | 0.997 | 0.927 | 1.000 | 0.709 | |
| rs112927755 | 4 | 40433460 | G | A | 0.940 | 7562 | 0.6 (0.1) | 4.32E-08 | 7.13E-08 | 0.997 | 0.927 | 1.000 | 0.775 | |
| WFT | rs59912956 | 3 | 69592250 | GA | GAA | 0.814 | 7446 | 1.0 (0.2) | 5.09E-10 | 2.46E-09 | 0.815 | 0.828 | 0.805 | 0.434c |
| rs568391433 | 6 | 33004530 | C | CT | 0.996 | 7446 | −5.8 (1.0) | 1.07E-08 | 5.09E-08 | 1.000 | 0.995 | 1.000 | 0.356c | |
| DSST | rs74610382 | 10 | 16254360 | G | A | 0.997 | 7372 | 10.8 (1.8) | 5.04E-09 | 1.32E-06 | 1.000 | 1.000 | 0.985 | 0.330 |
| rs116623781 | 10 | 16226698 | G | A | 0.997 | 7372 | 10.3 (1.8) | 5.05E-09 | 2.05E-06 | 1.000 | 1.000 | 0.984 | 0.310 | |
| rs181182078 | 10 | 16260622 | A | T | 0.997 | 7372 | 10.7 (1.8) | 5.94E-09 | 1.88E-06 | 1.000 | 1.000 | 0.985 | 0.658 | |
| rs150206471 | 10 | 16220142 | C | T | 0.997 | 7372 | 10.4 (1.8) | 7.44E-09 | 6.27E-07 | 1.000 | 1.000 | 0.984 | 0.327 | |
| rs142289140 | 10 | 16264277 | C | G | 0.997 | 7372 | 10.5 (1.8) | 8.31E-09 | 2.91E-06 | 1.000 | 1.000 | 0.985 | 0.786 | |
| rs115696258 | 10 | 16270189 | C | T | 0.997 | 7372 | 10.5 (1.8) | 1.11E-08 | 3.47E-06 | 1.000 | 1.000 | 0.986 | 0.379 | |
aEthnic groups used in replication were determined by estimated ancestry-specific allele frequency (in bold).
bReplication P-values were generated by meta-analysis of ARIC, CARDIA and HRS. The direction of association with the effect allele for all variants are the same in the discovery and replication samples.
cThe two variants for WFT were only observed in HRS so that the meta-analysis P-values were contributed solely by HRS. B-SEVLT brief Spanish English verbal learning test, WFT word fluency test, DSST digit symbol substitution test, chr chromosome, N sample size, SE standard error, edu-adj education adjusted, ARIC atherosclerosis risk in communities, CARDIA coronary artery risk development in young adults, HRS health and retirement study.