Table 2.
Allele frequency for risk variants in nephrotic syndrome (NS) vs. controls.
| SNP | Risk allele | Gene | MAF published controlsb | Risk AF: controls risk/total (frequency) | Risk AF: NS cases risk/total (frequency) | OR (95% CI) | p-valuea |
|---|---|---|---|---|---|---|---|
| rs1129740 | A | HLA-DQA1 | A = 0.49 (6) | 94,628/191,328 (0.50) | 1,251/1,784 (0.70) | 2.4 (2.2–2.7) | <2.2 × 10−16* |
| rs9348883 | A | BTNL2 | T = 0.94 (7) | 15,739/264,690 (0.06) | 330/1,756 (0.19) | 3.7 (3.2–4.1) | <2.2 × 10−16* |
| rs4642516 | T | HLA-DR/DQ | G = 0.27 (9) | 138,950/264,690 (0.52) | 1,211/1,752 (0.69) | 2.0 (1.8–2.2) | <2.2 × 10−16* |
| rs3134996 | A | HLA-DR/DQ | A = 0.28 (9) | 94,736/264,690 (0.36) | 1,494/1,762 (0.85) | 10.0 (8.8–11.4) | <2.2 × 10−16* |
| rs9273371 | T | Intergenic | NP (8) | 67,317/264,690 (0.25) | 736/1,764 (0.42) | 2.1 (1.9–2.3) | <2.2 × 10−16* |
| rs2637678 | T | CALHM6 | C = 0.40 (8) | 167,819/264,690 (0.63) | 1,329/1,766 (0.75) | 1.8 (1.6–2.0) | <2.2 × 10−16* |
| rs56117924 | A | NPHS1/KIRREL | A = 0.17 (10) | 14,543/264,690 (0.06) | 125/1,764 (0.07) | 1.3 (1.1–1.6) | 3.5 × 10−3* |
| rs6478109 | G | TNFSF15 | A = 0.39 (10) | 224,655/328,718 (0.68) | 1,393/1,762 (0.79) | 1.7 (1.6–2.0) | <2.2 × 10−16* |
| rs34213471 | A | TNFRSF11A | A = 0.31 (10) | 14,311/264,690 (0.05) | 207/1,766 (0.12) | 2.3 (2.0–2.7) | <2.2 × 10−16* |
SNP, single nucleotide polymorphism; NP, not published.
*
Significance after Bonferroni correction with α = 0.05.
a
P-values from chi square test of independence.
b
References for MAF published data controls are next to each AF.