Table 8. Top SNPs with p-values <10− 5 from MH test, and corresponding genes and p-values from Case-Control study, dTDT, Unphased association analysis, and IQS with threshold on dosage probabilities above 0.0 or 0.8.
| SNP | CHR | Position | Associated Gene | MH test p-value | Case-Control p-value | dTDT p-value | MAF | Unphased Wave I&II | IQS (>0) | IQS (>.8) |
| rs12116935 | 1 | 36,562,133 | FAM176B | 6.98E-06 | 6.56E-04 | 1.04E-03 | 0.38 | 6.77E-01 | 0.21 | 0.91 (395) |
| rs11583322 | 1 | 36,594,899 | STK40 | 1.10E-08 | 7.39E-06 | 1.04E-04 | 0.38 | 8.54E-01 | 0.20 | 0.85 (345) |
| rs1932933 | 1 | 160,384,670 | NOS1AP | 5.82E-06 | 1.99E-04 | 4.24E-03 | 0.37 | 6.85E-01 | 0.22 | 0.95 (478) |
| rs10801629 | 1 | 196,110,990 | 4.13E-06 | 1.18E-04 | 9.62E-03 | 0.40 | (482) | |||
| rs10922323 | 1 | 196,128,944 | 6.46E-06 | 1.52E-04 | 1.23E-02 | 0.40 | 9.54E-01 | 0.31 | 0.91 (550) | |
| rs1850344 | 3 | 108,667,763 | 8.16E-06 | 1.33E-04 | 2.08E-02 | 0.38 | 1.13E-01 | 0.21 | 0.92 (350) | |
| rs4384980 | 3 | 183,941,763 | 5.78E-07 | 9.17E-05 | 6.93E-04 | 0.42 | 4.46E-01 | 0.21 | 0.90 (405) | |
| rs2857839 | 4 | 3,006,428 | GRK4 | 6.60E-06 | 1.11E-03 | 5.56E-04 | 0.39 | (471) | ||
| rs1801058 | 4 | 3,008,948 | GRK4 | 6.48E-06 | 9.67E-04 | 6.57E-04 | 0.39 | 5.62E-01 | 0.22 | 0.89 (564) |
| rs2798303 | 4 | 3,010,385 | GRK4 | 1.28E-06 | 2.17E-04 | 8.55E-04 | 0.42 | 8.24E-01 | 0.22 | 0.91 (615) |
| rs994029 | 9 | 88,565,134 | 1.98E-07 | 3.62E-04 | 1.18E-05 | 0.37 | 3.59E-01 | 0.21 | 0.89 (713) | |
| rs2398236 | 10 | 5,321,159 | 9.07E-06 | 7.15E-04 | 1.96E-03 | 0.40 | 5.04E-01 | 0.22 | 0.90 (362) | |
| rs9423593 | 10 | 5,322,349 | 8.32E-06 | 1.04E-03 | 5.20E-04 | 0.37 | 9.04E-01 | 0.22 | 0.89 (381) | |
| rs7076488 | 10 | 5,323,008 | 2.13E-06 | 2.03E-04 | 1.49E-03 | 0.41 | (562) | |||
| rs3781458 | 10 | 126,333,921 | FAM53B | 4.27E-06 | 2.70E-03 | 1.31E-05 | 0.37 | (729) | ||
| rs3781452 | 10 | 126,345,119 | FAM53B | 6.86E-06 | 3.43E-03 | 1.81E-05 | 0.37 | (449) | ||
| rs1503452 | 11 | 16,408,708 | SOX6 | 3.21E-06 | 2.58E-04 | 1.80E-03 | 0.37 | 5.38E-02 | 0.22 | 0.89 (477) |
| rs3924047 | 11 | 70,507,506 | SHANK2 | 8.77E-06 | 2.19E-04 | 1.04E-02 | 0.44 | 4.95E-01 | 0.21 | 0.87 (489) |
| rs4356270 | 12 | 90,843,346 | 8.42E-06 | 8.12E-06 | 1.91E-01 | 0.35 | (370) | |||
| rs12427267 | 12 | 90,848,103 | 6.00E-07 | 6.04E-05 | 1.90E-03 | 0.38 | 2.15E-01 | 0.19 | 0.95 (403) | |
| rs11106345 | 12 | 90,850,631 | 7.22E-06 | 8.83E-06 | 1.81E-01 | 0.35 | (511) | |||
| rs10848190 | 12 | 129,767,988 | 5.43E-06 | 4.83E-04 | 2.36E-03 | 0.39 | (327) | |||
| rs1035717 | 14 | 69,648,452 | SLC8A3 | 6.36E-06 | 1.32E-03 | 2.19E-04 | 0.41 | 7.12E-01 | 0.23 | 0.95 (334) |
| rs4903712 | 14 | 77,685,346 | 1.67E-06 | 3.40E-05 | 1.79E-02 | 0.27 | 1.99E-03 | 0.29 | 0.92 (768) | |
| rs17754467 | 14 | 77,692,276 | 5.54E-07 | 3.20E-06 | 4.50E-02 | 0.23 | 7.36E-02 | 0.20 | 0.87 (621) | |
| rs1568447 | 17 | 70,348,607 | 4.08E-06 | 5.26E-04 | 1.13E-03 | 0.38 | (623) | |||
| rs9901283 | 17 | 70,349,427 | GRIN2C | 9.31E-06 | 8.18E-04 | 1.67E-03 | 0.38 | (397) | ||
| rs11652088 | 17 | 70,351,427 | GRIN2C | 3.50E-06 | 4.58E-04 | 1.00E-03 | 0.38 | 7.25E-01 | 0.16 | 0.82 (537) |
| rs8111589 | 19 | 50,726,398 | OPA3 | 8.27E-06 | 7.50E-05 | 4.03E-02 | 0.44 | 6.08E-01 | 0.21 | 0.90 (443) |
| rs2830045 | 21 | 26,380,280 | APP | 6.31E-06 | 1.77E-03 | 2.22E-04 | 0.37 | (396) | ||
| VARIANCE | 9.09E-12 | 8.60E-07 | 2.01E-03 | |||||||
| MEAN | 5.04E-06 | 6.94E-04 | 1.71E-02 |
Markers without Unphased and IQS data were not genotyped through the experimental validation. Numbers in the brackets next to the IQS (>0.8) column are the numbers of individuals who meet such restriction on that specific marker.