Table 1.
Meta-analysis association results from GWAS discovery sample and replication genotyping
| SNP | Chr | Position | A1:A2 | MAF | Number of associated SNPs | Tufts/MGH P | Tufts/MGH replication P | MPM P | Replication cohort P | Meta Z score | Meta OR | 95% CI | Final P |
| rs9621532 | 22 | 31414511 | C:A | 3.5% | 1 | 4.47E-02 | 3.28E-02 | N/A | 6.53E-08 | 5.897 | 0.62 | 0.53–0.73 | 3.71E-09*†‡§¶ |
| rs493258 | 15 | 56475172 | T:C | 44.8% | 3 | 4.53E-05 | 1.44E-01 | 9.98E-03 | 2.36E-03 | 5.650 | 0.86 | 0.82–0.91 | 1.61E-08*†‡§¶ |
| rs11755724 | 6 | 7063989 | A:G | 35.5% | 1 | 5.74E-04 | 1.34E-02 | 4.84E-02 | 3.12E-02 | 4.894 | 0.87 | 0.88–0.92 | 9.88E-07*†‡§¶ |
| rs13095226 | 3 | 100878962 | C:T | 11.6% | 3 | 5.03E-04 | 2.38E-01 | 1.16E-01 | 3.35E-03 | 4.708 | 1.24 | 1.13–1.35 | 2.50E-06*†‡§¶ |
| rs509859 | 6 | 116529937 | T:G | 38.2% | 5 | 5.18E-04 | 8.41E-01 | 2.13E-03 | 1.40E-01 | 4.124 | 0.92 | 0.89–0.96 | 3.73E-05*†‡§¶ |
| rs3748391 | 16 | 85846518 | G:T | 47.1% | 2 | 7.30E-04 | 7.28E-02 | 6.57E-02 | 2.24E-01 | 3.946 | 1.12 | 1.06–1.18 | 7.95E-05*†‡§¶ |
| rs12637095 | 3 | 119674993 | T:A | 19.6% | 2 | 9.39E-05 | 4.01E-01 | 3.41E-02 | 4.07E-01 | 3.716 | 0.90 | 0.84–0.95 | 2.03E-04*†‡§¶ |
SNP, single nucleotide polymorphism; Chr, chromosome; position/base-pair position in National Center for Biotechnology Information 36.1; A1, minor allele; A2, major allele; MAF, minor-allele frequency; number of associated SNPs, number of other SNPs in the region showing association in our discovery scan; Tufts/MGH P, P value of our original GWAS scan; Tufts/MGH replication P, P value of Tufts/MGH replication cohort; MPM P, P value of Michigan/Penn/Mayo GWAS; replication cohort P, P value of total combined weighted average of the meta-analysis Z score across the individual replication cohort sites; Meta Z score, weighted Z score used to combine the association from all cohorts calibrated on the theoretic power for a balanced case-control study design; meta OR, odds ratio for AMD combining all cohorts - A1 compared with A2; 95% CI, confidence interval for meta OR; final P, P value of all cohorts listed in the table plus the replication cohorts based upon the meta Z score.
*Johns Hopkins University;
†Columbia University;
‡University of Utah;
§Hopital Intercommunal de Creteil;
¶Washington University.