Table 1.
Most strongly associated SNPs using different methods to control for admixture and replication p-values.
| Analysis | SNP/Allele | Location | MAF | Multidimensional Scaling | LAMP-Adjusted | Genomic Control | |||
|---|---|---|---|---|---|---|---|---|---|
| OR | p-value | OR | p-value | OR | p-value | ||||
| AA only | rs2111504/Ta | DPY19L3 (19q13.11) | 0.23 | 1.74 | 1.5 × 10-6 | 1.73 | 1.7 × 10-6 | 1.66 | 5.0 × 10-6 |
| rs2769605/Tb | NTRK2 (9q21.33) | 0.22 | 0.60 | 4.5 × 10-5 | 0.61 | 4.5 × 10-5 | 0.63 | 1.5 × 10-4 | |
| EA only | rs1825828/Ca,c | 3q11.2 | 0.26 | 0.70 | 7.0 × 10-7 | 0.70 | 7.6 × 10-7 | 0.68 | 2.9 × 10-7 |
| rs5907577/Ta | Xq27.1 | 0.31 | 1.48 | 1.6 × 10-6 | 1.47 | 2.1 × 10-6 | 1.444 | 4.6 × 10-6 | |
| rs10193871/Gb | NAP5 (2q21.2) | 0.13 | 0.65 | 9.8 × 10-6 | 0.65 | 7.1 × 10-6 | 0.65 | 8.8 × 10-6 | |
| EA/AA combined (main effect) | rs4825220/Ca | Xq27.1 | 0.37 | 0.71 | 2.6 × 10-7 | 0.70 | 1.9 × 10-7 | 0.61 | 0.8496d |
| EA Pritzker Non-Overlap | rs6046396/Ga | RIN2 (20p11.23) | 0.29 | 1.54 | 1.43 × 10-6 | 1.56 | 6.2 × 10-7 | 1.57 | 4.93 × 10-7 |
a
Overall top hit
b
Top hit in region with at least 5 SNPs at P < 1× 10-4
c
Possibly of poor genotype quality (see text and Figure S2)
d
This p-value likely reflects the imbalance in the ratio of cases and controls in the EA relative to the AA sample.