Table 3.
Top 25 results from GWAS for SCZ in the CATIE study †
| SNP data | Gene data | Logistic regression tests for association | Allele frequency data | HapMap Allele FreqsComments ‡ | Context | SNP annotations | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP ID | Chromosome | Position | Transcripts in which SNP locate | Odds Ratio | Wald test | p-value | q-value | Rank | AFR odds ratio | EUR odds ratio | Cases | Controls | CATIE AFR | CATIE EUR | AFR/YRI | EUR/CEU | SNPs with p<0.0 | Proxy SNP ≤0.00 | CNV | Conserved p95 | Regulatory potential | Transfactor binding site | |
| rs4846033 | 1 | 11,722,830 | 0.348 | −4.594 | 4.36E-06 | 0.56 | 3 | 0.401 | 0.146 | 0.025 | 0.053 | 0.103 | 0.009 | 0.179 | 0.009 | 1 | Isolated finding | No | no | no | Yes | no | |
| rs10911902 | 1 | 183,363,974 | 0.560 | −4.770 | 1.85E-06 | 0.45 | 2 | 0.627 | 0.523 | 0.099 | 0.171 | 0.046 | 0.173 | 0.000 | 0.200 | 2 SNPs, 0.4 kb | No | no | no | Yes | Yes | ||
| rs9309325 | 2 | 60,492,482 | 0.727 | −4.076 | 4.58E-05 | 0.85 | 22 | 0.704 | 0.770 | 0.382 | 0.455 | 0.414 | 0.414 | 0.433 | 0.458 | 6 SNPs, 7 kb | Yes | Yes | Yes | Yes | no | ||
| rs1569351 | 3 | 60,287,457 | FHIT | 0.697 | −4.225 | 2.39E-05 | 0.85 | 11 | 0.609 | 0.729 | 0.337 | 0.415 | 0.173 | 0.470 | 0.192 | 0.433 | 12 SNPs, 31 kb | Yes | Yes | no | Yes | no | |
| rs4568102 | 3 | 72,070,679 | 4.118 | 4.103 | 4.08E-05 | 0.85 | 19 | 4.947 | 0.663 | 0.035 | 0.008 | 0.062 | 0.003 | 0.117 | 0.000 | 1, 2 | 2 SNPs, 5 kb | Yes | no | no | Yes | no | |
| rs1380272 | 4 | 21,431,975 | KCNIP4 | 0.522 | −4.397 | 1.10E-05 | 0.74 | 7 | 0.425 | 0.610 | 0.057 | 0.107 | 0.074 | 0.088 | 0.033 | 0.102 | 6 | 4 SNPs, 18 kb | Yes | no | no | Yes | no |
| rs1495716 | 4 | 177,103,725 | GPM6A | 1.423 | 4.223 | 2.41E-05 | 0.85 | 12 | 1.915 | 1.277 | 0.365 | 0.296 | 0.208 | 0.391 | 0.142 | 0.425 | 2 SNPs, 8 kb | No | no | no | no | no | |
| rs9295938 | 6 | 31,061,084 | C6orf205 | 1.642 | 4.138 | 3.51E-05 | 0.85 | 16 | 1.288 | 1.769 | 0.143 | 0.097 | 0.072 | 0.143 | 0.033 | 0.192 | 7 SNPs, 17 kb | No | no | no | no | no | |
| rs9400690 | 6 | 114,453,545 | 1.534 | 4.052 | 5.08E-05 | 0.85 | 24 | 1.588 | 1.635 | 0.193 | 0.151 | 0.057 | 0.230 | 0.000 | 0.267 | 3 SNPs, 6 kb | No | no | no | no | no | ||
| rs16917897 | 10 | 52,856,709 | D45864 PRKG1 Y07512 BC062 | 2.750 | 4.078 | 4.55E-05 | 0.85 | 21 | 2.864 | 1.650 | 0.049 | 0.019 | 0.099 | 0.005 | 0.119 | 0.000 | 1, 6 | Isolated finding | No | no | no | Yes | no |
| rs297257 | 10 | 127,298,704 | 0.689 | −4.129 | 3.64E-05 | 0.85 | 17 | 0.727 | 0.705 | 0.452 | 0.498 | 0.805 | 0.318 | 0.883 | 0.367 | 3 SNPs, 12 kb | Yes | no | no | Yes | no | ||
| rs9512730 | 13 | 26,975,144 | 1.515 | 4.586 | 4.52E-06 | 0.56 | 4 | 1.724 | 1.385 | 0.274 | 0.211 | 0.212 | 0.262 | 0.229 | 0.263 | 6 SNPs, 38 kb | Yes | no | no | no | no | ||
| rs942348 | 13 | 26,976,147 | 0.718 | −4.194 | 2.74E-05 | 0.85 | 14 | 1.641 | 1.399 | 0.451 | 0.521 | 0.311 | 0.547 | 0.220 | 0.500 | no | no | Yes | no | ||||
| rs17070578 | 13 | 78,431,983 | 1.903 | 4.069 | 4.72E-05 | 0.85 | 23 | 1.560 | 1.589 | 0.080 | 0.052 | 0.029 | 0.092 | 0.008 | 0.117 | 6 | 3 SNPs, 9 kb | No | no | no | no | no | |
| rs17095545 | 14 | 58,555,364 | 1.648 | 4.204 | 2.62E-05 | 0.85 | 13 | 1.501 | 1.746 | 0.153 | 0.099 | 0.205 | 0.094 | 0.217 | 0.100 | Isolated finding | No | no | no | no | no | ||
| rs7144633 | 14 | 58,582,146 | 1.784 | 4.309 | 1.64E-05 | 0.81 | 10 | 1.246 | 1.987 | 0.117 | 0.076 | 0.095 | 0.102 | 0.100 | 0.100 | Isolated finding | No | no | no | no | no | ||
| rs16977195 | 15 | 84,785,244 | AGBL1 | 6.005 | 4.785 | 1.71E-06 | 0.45 | 1 | 2.028 | 6.801 | 0.035 | 0.006 | 0.003 | 0.028 | 0.000 | 0.017 | 1 | 2 SNPs, 0.6 kb | No | no | no | Yes | no |
| rs234993 | 16 | 20,555,145 | ACSM1 BUCS1 | 0.524 | −4.036 | 5.44E-05 | 0.85 | 25 | 0.263 | 0.596 | 0.049 | 0.091 | 0.034 | 0.083 | 0.017 | 0.042 | 2 SNPs, 0.4 kb | No | no | no | Yes | no | |
| rs151222 | 16 | 20,581,993 | ACSM1 BUCS1 | 0.477 | −4.524 | 6.08E-06 | 0.57 | 5 | 0.310 | 0.549 | 0.045 | 0.093 | 0.038 | 0.080 | 0.017 | 0.042 | 3 SNPs, 2 kb | No | no | no | no | no | |
| rs17455133 | 18 | 49,719,513 | 0.643 | −4.142 | 3.44E-05 | 0.85 | 15 | 0.357 | 0.713 | 0.138 | 0.211 | 0.090 | 0.216 | 0.075 | 0.233 | 19 SNPs, 60 kb | Yes | no | no | Yes | no | ||
| rs2824301 | 21 | 17,738,145 | 0.720 | −4.103 | 4.09E-05 | 0.85 | 20 | 1.917 | 1.386 | 0.421 | 0.484 | 0.267 | 0.525 | 0.192 | 0.552 | 6 SNPs, 47 kb | Yes | no | no | Yes | no | ||
| rs10521865 | X | 146,501,918 | 0.550 | −4.125 | 3.70E-05 | 0.85 | 18 | 0.809 | 0.304 | 0.028 | 0.078 | 0.013 | 0.071 | 0.000 | 0.067 | 1, 3, 4, 6 | Isolated finding | No | no | no | Yes | no | |
| rs2159767 | X | 147,086,567 | 0.752 | −4.496 | 6.94E-06 | 0.57 | 6 | 0.288 | 0.753 | 0.430 | 0.549 | 0.274 | 0.618 | 0.144 | 0.678 | 5 | 2 SNPs 13 kb | Yes | no | no | Yes | no | |
| rs2536589 | X | 147,099,127 | 0.757 | −4.377 | 1.21E-05 | 0.74 | 8 | 0.285 | 0.762 | 0.412 | 0.529 | 0.291 | 0.639 | 0.156 | 0.678 | 5 | no | no | Yes | no | |||
| rs952515 | X | 147,142,998 | 0.759 | −4.321 | 1.56E-05 | 0.81 | 9 | 0.337 | 0.711 | 0.424 | 0.546 | 0.273 | 0.625 | 0.144 | 0.678 | 5 | 7 SNPs, 24 kb | Yes | no | no | Yes | no | |
†
All allele frequency data were standardized to the same reference alleles. Yellow boxes highlight issues of concern. Although SNPs with overall MAF<0.01 were dropped In the QC process, subgroups may have MAF<0.01. Some MAF>0.5 as the reference allele may be different in subgroups. EUR=European ancestry, AFR=African ancestry.
‡
1=rare allele, 2=direction of effects different in AFR and EUR subgroups, 3=low mean SNP quality scores, 4=greater SNP missingness in cases than controls, 5=frequency difference of >10% versus HapMap 6=suboptimal clustering of genotype groups on manual inspection of scatterplots