Table 2. Association results for Sweden-PGC meta-analysis, replication samples, and combined analysis.
| Chromosomal region | kb | SNPs | Index SNP | P-value | OR (SE) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs ID | a12 | bp | Freq | Sw+PGC | Replication | Combined | Sw+PGC | Replication | Combined | |||
| chr6:31,596,138-32,813,768 | 1217.6 | 1412 | rs114002140 | AG | 32,431,962 | 0.763 | 8.28x10−15 | 6.93×10−2 | 9.14×10−14 | 1.213 (0.025) | 1.070 (0.037) | 1.167 (0.021) |
| chr10:104,487,871-105,245,420 | 757.5 | 362 | rs7085104 | AG | 104,628,873 | 0.645 | 1.07×10−11 | 2.10×10−3 | 3.68×10−13 | 1.129 (0.018) | 1.076 (0.024) | 1.110 (0.014) |
| chr7:1,827,717-2,346,115 | 518.4 | 566 | rs6461049 | TC | 2,017,445 | 0.571 | 6.17×10−13 | 1.85×10−2 | 5.93×10−13 | 1.132 (0.017) | 1.059 (0.024) | 1.107 (0.014) |
| chr1:98,141,112-98,664,991 | 523.9 | 307 | rs1198588 | AT | 98,552,832 | 0.214 | 1.92×10−8 | 1.91×10−5 | 1.72×10−12 | 0.889 (0.021) | 0.888 (0.028) | 0.889 (0.017) |
| chr12:2,285,731-2,440,464 | 154.7 | 129 | rs1006737 | AG | 2,345,295 | 0.332 | 8.79×10−11 | 3.76×10−3 | 5.22×10−12 | 1.122 (0.018) | 1.070 (0.023) | 1.103 (0.014) |
| chr10:18,601,928-18,934,390 | 332.5 | 147 | rs17691888 | AG | 18,734,528 | 0.114 | 3.86×10−7 | 6.09×10−5 | 1.27×10−10 | 0.870 (0.028) | 0.842 (0.043) | 0.862 (0.023) |
| chr8:143,297,312-143,410,423 | 113.1 | 117 | rs4129585 | AC | 143,312,933 | 0.439 | 3.32×10−8 | 1.20×10−3 | 2.19×10−10 | 1.098 (0.017) | 1.077 (0.023) | 1.091 (0.014) |
| chr1:73,275,828-74,099,273 | 823.4 | 1026 | rs10789369 | AG | 73,824,909 | 0.383 | 4.68×10−7 | 1.99×10−4 | 3.64×10−10 | 1.091 (0.017) | 1.106 (0.027) | 1.095 (0.015) |
| chr11:130,706,918-130,894,976 | 188.1 | 269 | rs7940866 | AT | 130,817,579 | 0.513 | 1.61×10−10 | 1.30×10−1 | 1.83×10−9 | 0.896 (0.017) | 0.966 (0.023) | 0.921 (0.014) |
| chr5:151,888,959-152,835,304 | 946.3 | 79 | rs17504622 | TC | 152,654,479 | 0.050 | 6.88×10−8 | 1.02×10−2 | 2.65×10−9 | 1.250 (0.041) | 1.202 (0.072) | 1.238 (0.036) |
| chr19:19,354,937-19,744,079 | 389.1 | 294 | rs2905424 | TC | 19,473,445 | 0.348 | 5.38×10−7 | 1.64×10−3 | 3.44×10−9 | 1.092 (0.018) | 1.093 (0.028) | 1.092 (0.015) |
| chr2:37,422,072-37,592,628 | 170.6 | 10 | rs2373000 | TC | 37,592,628 | 0.402 | 9.17×10−6 | 1.38×10−4 | 6.78×10−9 | 1.079 (0.017) | 1.108 (0.027) | 1.087 (0.014) |
| chr5:101,581,848-101,870,822 | 289 | 367 | rs6878284 | TC | 101,769,726 | 0.637 | 1.47×10−6 | 1.61×10−3 | 9.03×10−9 | 0.917 (0.018) | 0.925 (0.025) | 0.920 (0.015) |
| chr3:52,215,002-53,175,017 | 960 | 533 | rs4687552 | TC | 52,838,402 | 0.641 | 9.31×10−7 | 3.23×10−3 | 1.16×10−8 | 1.092 (0.018) | 1.074 (0.024) | 1.086 (0.014) |
| chr2:145,139,727-145,214,607 | 74.9 | 4 | rs12991836 | AC | 145,141,541 | 0.652 | 2.25×10−6 | 1.30×10−3 | 1.19×10−8 | 0.918 (0.018) | 0.928 (0.023) | 0.922 (0.014) |
| chr2:200,628,118-201,293,421 | 665.3 | 249 | rs2949006 | TG | 200,715,388 | 0.192 | 4.67×10−9 | 9.18×10−2 | 1.21×10−8 | 1.132 (0.021) | 1.049 (0.029) | 1.102 (0.017) |
| chr18:52,722,378-52,827,668 | 105.3 | 39 | rs4801131 | TC | 52,752,700 | 0.418 | 6.46×10−6 | 5.27×10−4 | 1.22×10−8 | 0.926 (0.017) | 0.924 (0.023) | 0.925 (0.014) |
| chr2:233,550,961-233,808,241 | 257.3 | 197 | rs778371 | AG | 233,743,109 | 0.719 | 5.66×10−7 | 5.93×10−3 | 1.51×10−8 | 0.911 (0.019) | 0.935 (0.025) | 0.920 (0.015) |
| chr1:243,593,066-244,025,999 | 432.9 | 133 | rs14403 | TC | 243,663,893 | 0.227 | 1.35×10−8 | 8.34×10−2 | 1.80×10−8 | 0.889 (0.021) | 0.952 (0.029) | 0.910 (0.017) |
| chr12:123,447,928-123,913,433 | 465.5 | 353 | rs11532322 | AG | 123,731,423 | 0.318 | 1.37×10−6 | 4.77×10−3 | 2.28×10−8 | 1.099 (0.020) | 1.084 (0.029) | 1.094 (0.016) |
| chr1:243,418,063-243,627,135 | 209.1 | 115 | rs1538774 | CG | 243,544,827 | 0.260 | 6.11×10−7 | 8.38×10−3 | 2.53×10−8 | 0.907 (0.020) | 0.934 (0.026) | 0.917 (0.016) |
| chr8:89,188,454-89,761,163 | 572.7 | 402 | rs11995572 | TG | 89,592,083 | 0.135 | 5.39×10−8 | 5.02×10−2 | 3.33×10−8 | 1.150 (0.026) | 1.069 (0.034) | 1.120 (0.021) |
| chr5:60,484,179-60,843,706 | 359.5 | 100 | rs171748 | AG | 60,499,131 | 0.471 | 1.62×10−6 | 5.36×10−3 | 3.78×10−8 | 1.084 (0.017) | 1.068 (0.024) | 1.078 (0.014) |
| chr5:152,505,453-152,707,306 | 201.9 | 8 | rs2910032 | TC | 152,540,354 | 0.531 | 8.90×10−6 | 1.22×10−3 | 4.12×10−8 | 0.928 (0.017) | 0.916 (0.027) | 0.925 (0.014) |
| chr2:185,533,580-186,057,716 | 524.1 | 50 | rs4380187 | AC | 185,811,940 | 0.529 | 5.14×10−7 | 1.98×10−2 | 5.66×10−8 | 1.089 (0.017) | 1.056 (0.024) | 1.078 (0.014) |
| chr17:2,015,612-2,256,111 | 240.5 | 252 | rs4523957 | TG | 2,208,899 | 0.616 | 3.01×10−7 | 2.66×10−2 | 5.69×10−8 | 1.096 (0.018) | 1.057 (0.025) | 1.083 (0.015) |
| chr3:36,834,099-36,964,583 | 130.5 | 66 | rs6550435 | TG | 36,864,489 | 0.656 | 1.65×10−6 | 8.24×10−3 | 5.86×10−8 | 0.917 (0.018) | 0.939 (0.024) | 0.925 (0.014) |
We used LD “clumping” to aggregate association findings into genomic regions. The first three columns describe the genomic regions and the next three columns the index SNP, the SNP with strongest association in the genomic region. The next three columns show the P-values in the meta-analysis of Sw1-6 with the PGC schizophrenia results, the replication samples alone, and the final combined analysis of Sw1-6, PGC, and replication samples. The final three columns show the odd ratios (OR) and standard errors (SE). All locations UCSC hg19.