Table 1.
Individual SNP Associations Spanning Introns 3 – 6
| Genomic Information | BGT (644 trios) | PITT (491/540) | MGS (1345/1193) | CATIE (410/410) | ISC (2794/2976)* | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| ||||||||||||||||
| Cluster | SNP | BP | Region | alleles | Freq | P | O.R. | P | O.R. | P | O.R. | P | O.R. | MAF | P | O.R. |
| 2 | rs37020 | 1471374 | intron_6 | G/T | 0.45 | 0.01 | 0.79 | 0.006 | 0.78 | 0.54 | - | 0.27 | - | 0.438 | 0.409 | - |
| 2 | rs464049 | 1476905 | intron_4 | G/A | 0.45 | 0.04 | 0.83 | 0.007 | 0.78 | 0.49 | 1.04 | 0.24 | 0.89 | 0.438 | 0.358 | 1.04 |
| 2 | rs250686 | 1478159 | intron_4 | G/A | 0.45 | 0.007 | 0.78 | 0.54 | - | 0.26 | - | 0.436 | 0.383 | - | ||
| 1 | rs250682 | 1480803 | intron_4 | C/G | 0.22 | 0.004 | 0.69 | 0.19 | 1.10 | 0.50 | 0.92 | 0.210 | 0.076 | 1.09 | ||
| 2 | rs250681 | 1481011 | intron_4 | T/C | 0.45 | 0.007 | 0.78 | 0.50 | 1.04 | 0.25 | - | 0.437 | 0.592 | 1.02 | ||
| 1 | rs393795 | 1481514 | intron_4 | T/G | 0.22 | 0.004 | 0.70 | 0.11 | 1.11 | 0.53 | 0.93 | 0.210 | 0.101 | 1.14 | ||
| 1 | rs460700 | 1482969 | intron_4 | G/A | 0.22 | 0.004 | 0.70 | 0.14 | - | 0.43 | - | 0.209 | 0.079 | - | ||
| 2 | rs458334 | 1483093 | intron_4 | C/T | 0.45 | 0.02 | 0.81 | 0.007 | 0.77 | 0.47 | - | 0.26 | - | 0.563 | 0.451 | - |
| 1 | rs464061 | 1483244 | intron_4 | T/C | 0.25 | 0.05 | 0.8 | 0.004 | 0.70 | 0.10 | - | 0.25 | - | 0.224 | 0.080 | - |
| 1 | rs456082 | 1483515 | intron_4 | C/T | 0.22 | 0.09 | 0.85 | 0.004 | 0.70 | 0.14 | - | 0.45 | - | 0.213 | 0.086 | - |
| 1 | rs409588 | 1483834 | intron_4 | A/C | 0.22 | 0.004 | 0.71 | 0.14 | - | 0.45 | - | 0.213 | 0.088 | - | ||
| 1 | rs458860 | 1483933 | intron_4 | T/A | 0.22 | 0.004 | 1.41 | 0.14 | - | 0.46 | - | 0.213 | 0.087 | - | ||
| 1 | rs464528 | 1484123 | intron_4 | A/G/- | 0.22 | 0.004 | 0.71 | 0.14 | - | 0.46 | - | 0.213 | 0.087 | - | ||
| 1 | rs463379 | 1484164 | intron_4 | G/C | 0.22 | 0.07 | 0.83 | 0.004 | 0.71 | 0.14 | - | 0.46 | - | 0.213 | 0.091 | - |
| 1 | rs456774 | 1485202 | intron_4 | G/C | 0.23 | 0.005 | 0.71 | 0.14 | - | 0.33 | - | 0.225 | 0.081 | - | ||
| 1 | rs460000 | 1485825 | intron_3 | T/G | 0.22 | 0.006 | 0.75 | 0.14 | - | 0.46 | - | 0.213 | 0.088 | - | ||
| 1 | rs465130 | 1485876 | intron_3 | A/G | 0.21 | 0.002 | 0.72 | |||||||||
| 1 | rs458609 | 1487306 | intron_3 | A/G | 0.21 | 0.003 | 0.73 | |||||||||
| 1 | rs457702 | 1487430 | intron_3 | T/C | 0.21 | 0.003 | 0.73 | |||||||||
| 2 | rs462523 | 1488042 | intron_3 | T/C | 0.45 | 0.003 | 0.77 | |||||||||
| 2 | rs420422 | 1489408 | intron_3 | G/A | 0.45 | 0.01 | 0.8 | 0.012 | 0.80 | 0.41 | 1.05 | 0.2 | 0.88 | 0.445 | 0.499 | 1.03 |
BGT: Bulgarian families; PGH: Pittsburgh; MGS: Molecular Genetics of Schizophrenia; CATIE: Clinical Antipsychotic Trials of Intervention Effectiveness. ISC: International Schizophrenia Consortium. For each sample, numbers of cases/controls are listed below the acronym. Cluster: denotes LD clusters in this region (see supplementary figure SF1a). SNP: single nucleotide polymorphism; BP: genomic position (base pair); Alleles: SNP alleles, first letter denotes minor allele; Freq: frequency of minor allele in PITT sample; OR: Odds ratio for minor allele; ORs are shown in relation to the allele listed first for each SNP (minor allele). Results for imputed SNPs are italicized. Nominally significant associations at p<0.05 are bolded. SNP imputation was performed for the BGT sample, but software for formal association tests are currently unavailable. Some SNPs could not be imputed.
‘-’: ORs not listed for non-significant association imputation results.
Original ISC consortium data was filtered to remove the case-control data from the “Cardiff” site to prevent overlap with Bulgarian probands from the initial discovery sample.