Table 2.

Association analysis results for the top SNPs from the GWAS discovery + in silico replication analysis, selected for additional de novo replication

Stages rs61277444a
CHR 4rs7562121
CHR 2rs1989248
CHR 7rs72809865
CHR 10
Geneb: in PTPN13Geneb: in AFF3Geneb: 23kb to CNTNAP2Geneb: 350kb to NRG3
Pheno:c,dESRD Versus Non-ESRDPheno:dESRD Versus No DKDPheno:c,dESRD Versus Non-ESRDPheno:dCKD+DKDPheno:cESRD Versus No DKDPheno:cCombined DKD
Stage 1
 95% CI1.26 to 1.911.26 to 1.971.28 to 1.661.12 to 1.471.21 to 1.621.16 to 1.46
Stage 2
Stage 3
 N total11,665807911,4676220735812,540
 95% CI1.21 to 1.651.20 to 1.671.17 to 1.391.15 to 1.381.17 to 1.431.09 to 1.26
  • The association in FinnDiane was moderately attenuated from OR=1.49 (95% CI, 1.19 to 1.86; P=4.5×10−4; ESRD versus non-ESRD) and OR=1.50 (95% CI, 1.18 to 1.91; P=1×10−3; ESRD versus no DKD) with the imputed data to OR=1.36 (95% CI, 1.11 to 1.66; P=3.0×10−3; ESRD versus non-ESRD) and OR=1.40 (95% CI, 1.11 to 1.75; P=3.9×10−3; ESRD versus no DKD) using directly genotyped data. CHR, chromosome; Pheno, phenotypic comparison; N, number of cases/controls; EAF, effect allele frequency; 95% CI, 95% confidence interval.

  • a Because of moderate imputation quality at the discovery stage, rs61277444 was directly genotyped in 2913/3415 FinnDiane subjects.

  • b The closest gene/genes.

  • c Selection criteria for de novo replication: P value <10−6 for discovery + stage two meta-analysis.

  • d Selection criteria for de novo replication: P value <0.05 in the in silico replication for the phenotype selected for replication.