Table 2.
results of fatSNP phase 2 and schizophrenia Meta analysis
| Cardiff Full | REP1 | fatSNP2 | SZ Meta | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| cases n = 642 controls n = 2873 |
cases n = 1664 controls n = 3541 |
cases n = 2306 controls n = 6414 |
cases n = 18945 controls n = 38675 |
||||||||||
| SNP ID | class | Allele | r2 ( D') | OR | ARM | OR | CMH1 | OR | CMH | OR | P | ||
| rs12613195 | GWAS | C | 0.33 (0.75) | 1.35 | 1.20×10−5 | 1.09 | 0.038 | 1.17 | 6.03×10−5 | ||||
| rs17584522 | fatSNP | C | 0.24 (0.7) | 1.48 | 6.21×10−7 | 1.08 | 0.080 | 1.20 | 5.34×10−5 | ||||
| rs1344706 | GWAS | T | n/a | 1.38 | 7.08×10−7 | 1.09 | 0.026 | 1.18 | 8.31×10−6 | 1.10 | 2.54×10−11 | ||
| rs1583048 | eQTL | A | 0.36 (1) | 1.46 | 7.40×10−6 | 1.08 | 0.10 | 1.18 | 2.85×10−4 | ||||
| rs67264212 | tag nonsynonymous | C | 0.43 (0.95) | 1.21 | 0.0022 | 1.12 | 0.0050 | 1.15 | 1.06×10−4 | ||||
| rs124761473 | nonsynonymous | A | 0.43 (0.94) | 1.23 | 0.0055 | 1.11 | 0.011 | 1.14 | 6.54×10−4 | ||||
| ss177930705 | nonsynonymous | C | 0.01 (1) | 1.13 | 0.49 | 0.99 | 0.92 | 1.04 | 0.74 | ||||
| rs61739290 | nonsynonymous | G | 0.07 (1) | 1.31 | 0.017 | 1.03 | 0.36 | 1.12 | 0.099 | ||||
| rs3731834 | nonsynonymous | C | 0.19 (1) | 1.26 | 0.0080 | 1.02 | 0.36 | 1.09 | 0.072 | ||||
Cardiff Full = data from O'Donovan et al. 2008. REP1 = 3 replication samples (Bulgarian, Dublin 1 and Munich) combined, fatSNP2 = Cardiff Full plus REP1 samples combined and Sz Meta = meta analysis of all available schizophrenia samples.
Allele = associated allele in Cardiff Full. r2 ( D') = LD metrics pairwise with rs1344706. OR = Odds ratio. ARM =Armitage trend test P-value. CMH = Cochran-Mantel-Haenszel P-value.
1
1-tailed tests where OR are in the same direction as Cardiff Full.
2
intronic SNP assayed as a proxy for non-synonymous SNP rs4667001
3
UK extra Schizophrenia data unavailable.