Table 2.
Results from each GWAS phase where at least one result generated p<10−6. AA=African American; EA=European American; RAF=reference allele frequency; RSQ=imputation quality; genome wide significant results shown in bold, italicized font and underlined; p-values < 1×10−6. underlined; SNPs in bold were genotyped in phase 1; Meta=meta-analysis results.
| Case-Control Analysis | Phase 1 | Phase 2 | Phase 3 | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | SNP | Gene | AA P | EA P | Meta Phase 1 | RAF AA | RAF EA | RSQ AA | RSQ EA | AA P | EA P | RAF AA | RAF EA | RSQ AA | RSQ EA | AA P | EA P | RAF AA | RAF EA | Meta AA P | Meta EA P | Meta All P |
| 1 | rs200085570 | NA | 1.37E-01 | 2.89E-09 | 3.52E-06 | 0.97 | 0.96 | 0.71 | 0.83 | 7.32E-01 | 3.28E-01 | 0.96 | 0.96 | 0.76 | 0.88 | NA | NA | NA | NA | NA | NA | NA |
| 1 | rs6677435 | NA | 8.75E-01 | 2.18E-07 | 7.53E-04 | 0.99 | 0.96 | 0.77 | 0.84 | 8.36E-01 | 1.41E-01 | 0.98 | 0.96 | 0.980 | 0.98 | 5.05E-01 | 9.29E-01 | 0.02 | 0.05 | 8.61E-01 | 8.82E-06 | 3.23E-03 |
| 1 | rs116439821 | LGR6 | 2.71E-07 | NA | * | 0.96 | 1.00 | 0.91 | 0.91 | 5.67E-01 | NA | 0.96 | 1.00 | 0.94 | 0.00 | 4.53E-01 | NA | 0.04 | 1.00 | 1.55E-05 | NA | 1.55E-05 |
| 2 | rs72840936 | STEAP3 | 5.34E-01 | 8.43E-07 | 9.29E-03 | 0.98 | 0.96 | 0.87 | 0.96 | 6.29E-01 | 1.71E-01 | 0.98 | 0.96 | 0.90 | 0.99 | 9.84E-01 | 3.41E-01 | 0.01 | 0.04 | 4.61E-01 | 3.19E-06 | 7.22E-03 |
| 3 | rs111325002 | NA | 1.04E-07 | NA | * | 0.97 | 1.00 | 0.93 | 0.17 | 4.41E-01 | NA | 0.98 | 1.00 | 0.96 | 0.82 | NA | NA | NA | NA | 3.70E-07 | NA | 3.70E-07 |
| 4 | rs4861386 | UCHL1 | 4.14E-01 | 8.35E-07 | 1.96E-04 | 0.51 | 0.41 | 0.96 | 0.99 | 4.18E-01 | 4.51E-01 | 0.54 | 0.43 | 0.96 | 0.96 | 8.35E-01 | 7.70E-01 | 0.51 | 0.41 | 3.32E-01 | 1.61E-04 | 9.34E-04 |
| 4 | rs1757939 | SCLT1 | 7.88E-07 | 7.22E-01 | 2.88E-04 | 0.41 | 0.43 | 0.95 | 0.93 | 4.02E-01 | 9.64E-01 | 0.40 | 0.42 | 0.99 | 0.99 | 3.09E-01 | 9.45E-01 | 0.38 | 0.42 | 2.90E-05 | 8.05E-01 | 4.36E-03 |
| 4 | rs4129566 | NA | 4.26E-07 | 8.11E-01 | 4.29E-05 | 0.90 | 0.86 | 0.98 | 0.99 | 2.05E-01 | 8.16E-01 | 0.89 | 0.86 | 0.99 | 0.94 | 7.13E-01 | 1.92E-04 | 0.90 | 0.86 | 2.89E-06 | 5.49E-02 | 2.50E-06 |
| 4 | rs11944332 | RANP6 | 4.11E-07 | 8.03E-01 | 4.08E-05 | 0.90 | 0.86 | 0.98 | 0.99 | 2.08E-01 | 8.57E-01 | 0.89 | 0.86 | 0.99 | 0.94 | 9.19E-01 | 2.17E-04 | 0.91 | 0.86 | 1.86E-06 | 5.95E-02 | 2.06E-06 |
| 6 | rs6912117 | PXT1 | 4.54E-02 | 5.06E-07 | 2.51E-06 | 0.69 | 0.79 | 0.97 | 0.99 | 9.47E-01 | 3.96E-01 | 0.71 | 0.80 | 0.94 | 0.98 | 6.52E-01 | 8.54E-01 | 0.69 | 0.79 | 7.16E-02 | 1.60E-03 | 4.95E-04 |
| 6 | rs59955083 | PXT1 | 4.47E-02 | 5.67E-07 | 2.62E-06 | 0.69 | 0.79 | 0.97 | 0.99 | 9.29E-01 | 3.59E-01 | 0.71 | 0.80 | 0.94 | 0.99 | NA | NA | NA | NA | 8.09E-02 | 7.95E-04 | 3.86E-04 |
| 8 | rs75686122 | RIMS2 | 5.24E-07 | 4.98E-01 | 1.45E-05 | 0.96 | 0.91 | 0.97 | 0.97 | 7.68E-01 | 4.70E-01 | 0.97 | 0.91 | 0.95 | 1.00 | 3.03E-01 | 5.78E-01 | 0.02 | 0.08 | 2.83E-06 | 5.21E-01 | 1.30E-04 |
| 10 | rs34831910 | NA | 4.51E-01 | 6.78E-07 | 1.16E-02 | 0.98 | 0.87 | 0.96 | 0.98 | 8.57E-01 | 3.40E-01 | 0.98 | 0.85 | 0.95 | 1.00 | 3.47E-01 | 3.93E-01 | 0.04 | 0.13 | 6.86E-01 | 9.13E-03 | 1.31E-01 |
| 10 | rs7899919 | NA | 5.04E-01 | 3.30E-07 | 7.41E-03 | 0.98 | 0.87 | 0.97 | 1.00 | 6.67E-01 | 2.36E-01 | 0.98 | 0.86 | 0.96 | 0.98 | 8.78E-01 | 3.71E-01 | 0.04 | 0.13 | 4.25E-01 | 8.52E-04 | 8.36E-02 |
| 10 | rs9664175 | NA | 4.78E-01 | 1.98E-07 | 6.82E-03 | 0.98 | 0.87 | 0.96 | 1.00 | 6.84E-01 | 2.51E-01 | 0.98 | 0.86 | 0.96 | 0.98 | 3.94E-01 | 2.86E-01 | 0.03 | 0.13 | 2.93E-01 | 4.72E-04 | 9.74E-02 |
| 10 | rs7086629 | CHST3 | 7.40E-07 | NA | * | 0.96 | 1.00 | 0.99 | NA | 6.04E-01 | NA | 0.96 | 1.00 | 0.99 | NA | 7.32E-01 | 9.74E-01 | 0.96 | 1.00 | 5.11E-05 | NA | 1.93E-04 |
| 17 | rs2005290 | OR3A2/OR3A1 | 1.97E-03 | 1.41E-05 | 2.86E-07 | 0.15 | 0.06 | 0.79 | 0.66 | 4.43E-01 | 5.98E-02 | 0.14 | 0.04 | 0.80 | 0.65 | 6.16E-01 | 1.42E-01 | 0.35 | 0.14 | 1.49E-02 | 1.96E-06 | 4.47E-07 |
| 17 | rs114903983 | HSF5 | 4.10E-07 | NA | * | 0.94 | 1.00 | 0.99 | NA | 7.31E-01 | NA | 0.96 | 1.00 | 0.94 | NA | 3.00E-01 | 7.90E-01 | 0.95 | 1.00 | 1.56E-04 | NA | 3.26E-04 |
| 17 | rs116087723 | MTMR4 | 2.63E-07 | NA | * | 0.94 | 1.00 | 1.00 | NA | 6.16E-01 | NA | 0.96 | 1.00 | 0.96 | NA | 1.34E-01 | 7.90E-01 | 0.06 | 0.00 | 2.92E-04 | NA | 5.68E-04 |
| 18 | rs79794368 | MYL12A | 6.81E-07 | NA | * | 0.96 | 1.00 | 0.93 | NA | 4.16E-01 | NA | 0.96 | 1.00 | 0.88 | NA | 1.20E-01 | NA | 0.05 | 0.00 | 1.48E-05 | NA | 1.48E-05 |
| 18 | rs13381416 | MYL12A | 7.70E-07 | NA | * | 0.96 | 1.00 | 0.93 | NA | 4.13E-01 | NA | 0.96 | 1.00 | 0.88 | NA | 6.49E-02 | NA | 0.95 | 1.00 | 1.06E-05 | NA | 1.06E-05 |
| 18 | rs61751192 | MYL12A | 9.12E-07 | NA | * | 0.96 | 1.00 | 0.93 | NA | 4.12E-01 | NA | 0.96 | 1.00 | 0.89 | NA | 1.08E-01 | NA | 0.05 | 0.00 | 1.73E-05 | NA | 1.73E-05 |
| 18 | rs12956327 | FAM69C | 5.66E-07 | 7.84E-01 | 1.94E-04 | 0.93 | 0.81 | 0.86 | 0.93 | 8.50E-01 | 1.65E-01 | 0.93 | 0.81 | 0.80 | 0.93 | 9.26E-01 | 9.27E-01 | 0.06 | 0.17 | 1.57E-05 | 3.52E-01 | 1.33E-02 |
| Symptom count | ||||||||||||||||||||||
| 10 | rs2629540 | FAM53B | 3.78E-06 | 4.97E-03 | 7.64E-08 | 0.93 | 0.75 | 0.94 | 0.95 | 6.02E-02 | 9.44E-02 | 0.94 | 0.74 | 0.95 | 0.96 | 4.57E-01 | 4.87E-01 | 0.94 | 0.77 | 1.38E-06 | 2.62E-03 | 4.28E-08 |
| 12 | rs150954431 | NCOR2 | 5.36E-01 | 1.19E-09 | 1.23E-03 | 0.99 | 0.97 | 0.63 | 0.65 | 5.84E-01 | 1.47E-01 | 0.99 | 0.97 | 0.61 | 0.59 | 3.32E-01 | 1.83E-01 | 1.00 | 0.98 | 5.66E-01 | 5.35E-07 | 9.41E-04 |
| 16 | rs4782559 | CDH13 | 9.31E-07 | 8.11E-02 | 7.54E-07 | 0.22 | 0.46 | 0.90 | 0.97 | 7.90E-01 | 9.62E-01 | 0.25 | 0.47 | 0.83 | 0.93 | NA | NA | 1.00 | 1.00 | 1.82E-05 | 2.77E-01 | 1.54E-04 |
| Cocaine induced Paranoia | ||||||||||||||||||||||
| 10 | rs2456778 | CDK1 | 4.86E-08 | 5.02E-02 | 4.26E-08 | 0.25 | 0.26 | 0.98 | 0.98 | NA | NA | NA | NA | NA | NA | 1.58E-01 | 6.36E-01 | 0.23 | 0.23 | 4.77E-06 | 5.53E-02 | 2.586E-06 |