Table 2

Top loci (P < 1 × 10−5) associated with DPN: effects in ACCORD and validation in BARI 2D

SNPPosition‡Closest geneMA**Discovery set (ACCORD)Validation set (BARI 2D)ACCORD + BARI 2D*
MAF¶ 1000GMAF§ case subjectsMAF§ control subjectsOR (95% CI)PMAF case subjectsMAF control subjectsOR (95% CI)POR (95% CI)P
rs134177832:167629849XIRP2T0.140.140.200.64 (0.55–0.74)1.9 × 10−90.140.200.57 (0.41–0.80)0.00090.63 (0.55–0.72)7.9 × 10−12
rs129886692:240275570HDAC4C0.150.160.200.71 (0.62–0.82)2.7 × 10−60.160.131.22 (0.83–1.78)0.320.76 (0.66–0.87)5.1 × 10−5
rs607708803:8037416LOC101–927394A0.210.210.260.75 (0.66–0.84)5.0 × 10−60.200.210.93 (0.68–1.26)0.620.77 (0.68–0.86)1.0 × 10−5
rs119329464:45140214GUF1G0.120.120.160.69 (0.59–0.82)9.6 × 10−60.130.111.01 (0.68–1.49)0.980.73 (0.63–0.85)4.5 × 10−5
rs12026607:70658177WBSCR17T0.220.200.250.74 (0.65–0.84)6.2 × 10−60.230.260.81 (0.60–1.09)0.160.75 (0.67–0.85)2.5 × 10−6
rs132654308:4165607CSMD1A0.090.090.130.64 (0.52–0.76)1.0 × 10−60.110.091.35 (0.84–2.15)0.210.70 (0.59–0.83)4.3 × 10−5
rs249101910:70776987KIAA1279A0.450.470.401.31 (1.17–1.47)4.4 × 10−60.450.461.02 (0.79–1.32)0.861.25 (1.13–1.39)2.0 × 10−5
rs7749407411:132794801OPCMLT0.080.070.100.61 (0.50–0.74)1.0 × 10−60.070.061.28 (0.71–2.29)0.410.66 (0.54–0.79)1.3 × 10−5
rs20165591814:76791306ESRRBC0.280.260.320.75 (0.66–0.85)6.9 × 10−60.300.241.41 (1.02–1.96)0.040.81 (0.72–0.91)5.3 × 10−4
rs1107375215:88423051NTRK3C0.330.320.380.76 (0.67–0.85)2.1 × 10−60.330.360.80 (0.61–1.05)0.110.76 (0.68–0.85)6.5 × 10−7
rs994809518:12018665IMPA2C0.140.150.200.71 (0.61–0.82)3.6 × 10−60.140.160.88 (0.63–1.24)0.460.73 (0.64–0.84)5.4 × 10−6
rs10555080 (aka rs72397229)19:32043170THEG5ANA0.360.301.32 (1.17–1.49)6.9 × 10−60.380.321.46 (1.10–1.94)0.00981.34 (1.20–1.50)2.6 × 10−7
rs3494855821:42825856MX1A0.280.270.320.76 (0.67–0.85)4.7 × 10−60.300.311.01 (0.77–1.33)0.950.79 (0.71–0.88)3.0 × 10−5
  • In ACCORD, the primary model was adjusted by assignment to interventions, seven clinical center networks, and top three principal components. In BARI 2D, adjustments included assignment to interventions, country of origin, and top three principal components.

  • *Meta-analysis of results in the discovery and validation sets. ‡Position is chromosome:bp according to the National Center for Biotechnology Information assembly build GRCh37/hg19. **MA is minor or effect allele. §MAF in the discovery set is the average of minor allele frequencies in the two ACCORD genotyping sets (ANYSET and ACCSET). ¶MAF in 1000 Genomes Project Phase 3 European populations was derived from Ensembl GRCh37 Release 93 (http://grch37.ensembl.org/index.html).