Table 3 Region-based tests of candidate genes for lipid phenotypes
| Â | Gene-based analysis (p-values)a | Scan statistic analysis | |||||||
|---|---|---|---|---|---|---|---|---|---|
Lipid Gene | Chr. | No. SNPs (No. PCs) | Global LR test | Schaid test | James min Ptest | No. SNPs | Region p-value | GW rank | Empirical GW p-valueb |
HDL | |||||||||
   CETP | 16 | 7 (3) | 7.96 × 10 -28 | 3.32 × 10 -20 | 3.81 × 10 -16 | 22 | 4.72 × 10-17 | 2 | <1.0 × 10 -5 |
   LPL | 8 | 5 (3) | 7.54 × 10 -7 | 8.95 × 10 -7 | 8.52 × 10 -6 | 12 | 1.06 × 10-8 | 6 | 9.42 × 10 -4 |
   ABCA1 | 9 | 52 (14) | 1.67 × 10 -6 | 0.15 | 1.12 × 10-3 | 16 | 2.51 × 10-8 | 10 | 1.50 × 10 -3 |
   HERPUD1 | 16 | 2 (2) | 0.36 | 0.15 | 0.45 | 22 | 4.72 × 10-17 | 2 | <1.0 × 10 -5 |
   SLIT1 | 10 | 47 (10) | 4.27 × 10-4 | 1.87 × 10 -4 | 0.02 | 6 | 6.15 × 10-4 | 197 | 0.31 |
   LIPG | 18 | 1 (1) | 0.29 | 0.29 | 0.29 | 39 | 7.81 × 10-26 | 1 | <1.0 × 10 -5 |
   ACAA2 | 18 | 5 (2) | 0.67 | 0.42 | 0.61 | 39 | 7.81 × 10-26 | 1 | <1.0 × 10 -5 |
LDL | |||||||||
   PSRC1 | 1 | 1 (1) | 2.43 × 10 -25 | 2.43 × 10 -25 | 1.21 × 10 -25 | 3 | 4.20 × 10-6 | 218c | 0.02 |
   LDLR | 19 | 5 (2) | 2.67 × 10 -5 | 3.80 × 10 -5 | 9.91 × 10 -6 | 15 | 1.82 × 10-8 | 14 | 1.10 × 10 -3 |
   APOB | 2 | 10 (4) | 2.33 × 10 -11 | 5.41 × 10 -11 | 2.06 × 10 -9 | 17 | 9.40 × 10-10 | 7 | 2.22 × 10 -4 |
   HMGCR | 5 | 5 (2) | 5.52 × 10-4 | 1.09 × 10 -4 | 1.38 × 10-3 | NAd | NA | NA | NA |
   BCAM | 19 | 1 (1) | 0.09 | 0.09 | 0.09 | 18 | 6.09 × 10-11 | 3 | 4.69 × 10 -5 |
TG | |||||||||
   TBL2 | 7 | 3 (2) | 8.38 × 10 -14 | 2.78 × 10 -14 | 6.81 × 10 -12 | 7 | 4.64 × 10-10 | 106c | 4.75 × 10 -5 |
   LPL | 8 | 5 (3) | 3.23 × 10 -11 | 1.70 × 10 -11 | 1.84 × 10 -9 | 24 | 1.27 × 10-16 | 3 | <1.0 × 10 -5 |
   GCKR | 2 | 4 (2) | 8.98 × 10 -13 | 8.17 × 10 -10 | 2.46 × 10 -11 | 6 | 5.51 × 10-6 | 40 | 0.013 |