Table 2.
Variants showing nominal association with DR (P uncorrected < 0.05) in the current study among the SNPs previously associated with DR
| Phenotype | SNP | Chr | Position | A1 | A2 | Original association | Closest gene | Meta-analysis (WESDR + DCCT/EDIC) | Discovery vs. replication | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OR | P | References | FRQ | OR (95 % CI) | P meta* | Direction | P Het | ||||||||
| SDR | rs39059 | 7 | 29,221,995 | A | G | 1.29 | 2.6E−04 | Hu et al. (2011) | CHN2 | 0.63 | 0.78 (0.65–0.94) | 8.6E−03 | −−−− | 0.36 | +− |
| SDR | rs1571942 | 10 | 20,582,640 | A | G | 0.60 | 3.5E−07 | Huang et al. (2011) | PLXDC2 | 0.85 | 0.71 (0.55–0.91) | 6.4E−03 | −−−− | 0.67 | −− |
| SDR | rs12219125 | 10 | 20,633,093 | T | G | 1.62 | 9.3E−09 | Huang et al. (2011) | PLXDC2 | 0.15 | 1.40 (1.10–1.79) | 7.2E−03 | ++++ | 0.84 | ++ |
| MDR | rs1801282 | 3 | 12,368,125 | G | C | 0.81 | 3.0E−02 | Ma et al. (2012) | PPARG | 0.13 | 0.73 (0.57–0.93) | 9.7E−03 | −+−−− | 0.004 | −− |
Chr chromosome, Position physical position based on hg18, A1/A2 effect/other alleles, OR odds ratio for the effect allele, P the association P value in the original GWAS, FRQ effect allele frequency, P meta P value in the case–control meta-analysis unadjusted for multiple testing, Direction direction of effect in participating studies in this meta-analysis with this order, SDR WESDR, DCCT/EDIC primary cohort, secondary cohort—conventional treatment, secondary cohort—intensive treatment, MDR WESDR, DCCT/EDIC PRI cohort—conv. Rx, PRI cohort—intensive Rx, SEC cohort—conv. Rx, SEC cohort—intensive Rx, P Het P value of Cochran’s Q test for heterogeneity, Discovery vs. replication direction of effect in the original report (discovery) is compared with the current study (replication)
* The significance threshold adjusting for the effective number of test is P < 1.5 × 10−3