Table.
Nine Most Significantly Associated Single Nucleotide Polymorphisms
| SNP ID | Chromosome | Gene | Risk allele | Screening stage | Replication stage | Combined | |||
|---|---|---|---|---|---|---|---|---|---|
| P min (test model) | OR (95% CI) [RR vs (RP+PP)] | P recessive | OR (95%CI) [RR vs (RP+PP)] | P recessive | OR (95% CI) [RR vs (RP+PP)] | ||||
| rs11931074 | 4q22.1 | Downstream of SNCA | T | 1.7E–07(recessive)b | 5.4 (2.7–11.1) | 1.6E–04a | 6.6 (2.15–19.93) | 5.5E–12 | 6.2 (3.4–11.2) |
| rs3857059 | 4q22.1 | SNCA | G | 6.9E–04(recessive) | 3.8 (1.7–8.5) | 1.3E–06a | 9.8 (3.20–29.78) | 2.1E–10 | 5.9 (3.2–10.9) |
| rs9480154 | 6q25.1 | Downstream of PPP1R14C | A | 1.6E– 05(recessive)b | 5.0 (2.2–11.2) | 0.99 | 1.0 (0.12–8.81) | 1.3E–04 | 3.9 (1.8–8.2) |
| rs2794256 | 6q22.31 | LOC728727 | T | 1.7E–03(recessive) | 1.7 (1.2–2.5) | 0.17 | 1.6 (0.81–3.19) | 4.0E–04 | 1.7 (1.3–2.4) |
| rs2042079 | 2p24.2 | Intergenic | A | 2.7E–03(recessive) | 1.7 (1.2–2.5) | 0.21 | 1.6 (0.77–3.18) | 8.0E–04 | 1.7 (1.3–2.4) |
| rs13139027 | 4p16.2 | Upstream of MSX1 | A | 2.5E–03(recessive) | 3.9 (1.5–10.1) | 0.53 | 1.5 (0.41–5.63) | 1.8E–03 | 3.2 (1.5–6.9) |
| rs2515501 | 8p23.2 | MCPH1 | T | 6.5E–04(recessive) | 2.4 (1.4–4.1) | 0.45 | 0.6 (0.13–2.52) | 7.0E–03 | 1.9 (1.2–3.2) |
| rs2896159 | 7q31.2 | Intergenic | T | 3.0E–03(recessive) | 0.7 (0.5–1.1) | 0.38 | 1.3 (0.73–2.26) | 0.43 | 1.3 (1.1–1.6) |
| rs2856336 | 12p13.2 | ETV6 | C | 1.6E– 08(recessive)b | 4.6 (2.6–8.3) | 0.12 | —c | 2.4E–05 | 3.1 (1.8–5.5) |
a
Exceeded Bonferroni significance threshold in the replication stage (i.e., 0.05/10 = 0.005).
b
Exceeded Bonferroni significance threshold for multiple testing in the screening stage (i.e., 0.05/[384*5] = 2.6E−05).
c
Unable to calculate odds ratio (OR) because of low allele frequency in cases. SNP = single nucleotide polymorphism; CI = confidence interval; R = risk allele; P = protective allele; HWE = Hardy–Weinberg equilibrium.