Table 2.
eQTLs Unique to Global Ancestry Adjustment
| SNP Ref/Alt | Gene | eQTL P Value, No Adjustment | eQTL P Value, GA Adjustment | eQTL P Value, LA Adjustment | LA Association P Value | Alt Allele Frequency in YRI | Alt Allele Frequency in CEU |
|---|---|---|---|---|---|---|---|
| dbSNP: rs8044834 C/T | AMFR | 2.26 × 10−9 | 6.35 × 10−8 | 1.74 × 10−2 | 8.80 × 10−4 | 4% | 58% |
| dbSNP: rs2341000 G/T |
PLA2G4C | 3.01 × 10−8 | 1.12 × 10−7 | 5.81 × 10−2 | 7.17 × 10−3 | 100% | 46% |
| dbSNP: rs2814778 C/T |
ACKR1 | 2.43 × 10−44 | 1.67 × 10−17 | 4.77 × 10−1 | 1.99 × 10−44 | 0% | 99% |
Two eQTLs (dbSNP: rs8044834 and dbSNP: rs2341000) were found to have highly significant associations by the global ancestry (GA) adjustment method, but were non-significant according to the local ancestry (LA) adjustment method in the NIGMS dataset (marked dots in Figure 3A); similarly, one such eQTL (dbSNP: rs2814778) was found in the GTEx whole-blood dataset (marked dot in Figure 3C).
Included in the table are the p values of allelic association tests with no correction for ancestry, with GA adjustment, with LA adjustment, and with the p value of LA in the allelic association with LA adjustment. Allele frequencies are from 1000 Genomes Phase3 data. GA stands for global ancestry and LA stands for local ancestry.