Table 2.
Estimated ancestry-specific allele frequencies for SNVs identified in single variant test and SKAT WGS analyses using ASAFE.
| Chr:position (hg38) | SNV/indel (Gene) | Test | Estimated ancestry-specific allele frequencies |
||
|---|---|---|---|---|---|
| African | European | Native American | |||
| 19:3,799,817 | rs539182790 (MATK) | Single variant test | 3.1 × 10−10 | 7.9 × 10−4 | 2.2 × 10−2 |
| 16:79,599,332 | rs1230233783 (MAF) | SKAT | 1.4 × 10−8 | 4.2 × 10−8 | 2.0 × 10−7 |
| 11:102,593,550 | rs149589493 (MMP20) | SKAT | 7.4 × 10−3 | 2.4 × 10−8 | 8.9 × 10−11 |
| 6:44,376,382 | rs190658489 (SPATS1) | SKAT | 6.6 × 10−4 | 3.2 × 10−8 | 2.3 × 10−7 |
| 17:82,054,634 | rs78902137 (GPS1) | SKAT | 2.6 × 10−2 | 2.0 × 10−8 | 7.2 × 10−16 |
SNV, single nucleotide variant. MMP20, SPATS1, GSP1 genes had suggestive association in gene-based SKAT analyses. rs1230233783 alternative allele is more common in East Asians (see text).