Table 2.
Genome-wide significant loci from the EMMAX analysis and their significance in the original multiethnic analysis.
| Locus | EMMAX Analysis | The Multiethnic Meta-Analysis [19] | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Sentinel SNP | Chr:Pos | Ref/Alt | MAF | β (S.E.) | p-Value | Gene | Sentinel SNP | Meta OR † | p-Value | r2 ‡ | |
| 8q24 | rs72728755 | 8:129990382 | T/A | 0.16 | 0.08 (0.008) | 1.94 × 10−22 | Gene desert | rs17242358 | 2.00 [1.78–2.26] | 5.63 × 10−30 | 0.97 |
| 1q32.2 | rs2235370 | 1:209946027 | C/A | 0.13 | −0.05 (0.009) | 5.15 × 10−9 | TRAF3IP3 | rs11119345 | 1.81 [1.57–2.07] | 2.52 × 10−17 | 0.84 |
| rs2235373 | 1:209963803 | G/A | 0.26 | −0.04 (0.007) | 2.12 × 10−8 | IRF6 | 0.30 | ||||
| 2p24.2 | rs7552 | 2:16733928 | A/G | 0.50 | 0.04 (0.006) | 3.40 × 10−8 | FAM49A | rs7552 | 1.28 [1.17–1.40] | 4.22 × 10−8 | 1.00 |
| 17p13.1 | rs11273201 | 17:8930219 | AACCCAAAACCCAC/A | 0.27 | −0.04 (0.007) | 3.58 × 10−8 | NTN1 | rs11273201 | 1.44 [1.29–1.59] | 7.84 × 10−12 | 1.00 |
Chr = chromosome; Pos = position in base pairs (hg19); Ref = reference allele; Alt = alternate allele; MAF = minor allele frequency, S.E. = standard error of β. † Odds ratio from the meta-analysis of the case-parent trio analysis and case-control analysis. ‡ r2 LD statistics against all populations of 1000 Reference Genome.