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
 N813/3995813/2394813/39951117/2018813/23942563/2593
 EAF0.090.090.230.280.280.16
 OR1.551.581.461.281.401.30
 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
 P4.3×10−68.7×10−68.9×10−81.8×10−44.0×10−65.0×10−6
Stage 2
 N964/4806964/3187964/48061104/1981964/31872659/3842
 P2×10−33×10−30.041×10−30.020.05
Stage 3
 N94/99394/62767/822367/516
 P0.190.140.590.54
All
 N1871/97941871/62081844/96232221/39991777/55815589/6951
 N total11,665807911,4676220735812,540
 OR1.411.421.271.261.291.17
 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
 P1.9×10−66.0×10−63.5×10−76.0×10−71.8×10−67.4×10−6
  • 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.