Table 2.

Summary results of 25 SNPs using PRACTICAL and GWAS stage III datasets in European

Markera Chr/nearby geneAllelesb PositioncMAFdPer allelee OR (95%CI)Het ORe,f (95%CI)Hom ORe,g (95%CI)PhPi
rs721048 2/EHBP1C/T 631317310.181.11 (1.07–1.16)1.09 (1.04–1.15)1.32 (1.17–1.48)9.8 × 10−80.13
rs1465618 2/THADAG/A 435539490.21501.07 (1.03–1.11)1.08 (1.03–1.13)1.14 (1.03–1.26)1.9 × 10−40.39
rs12621278 2/ITGA6A/G 1733115530.060.75 (0.70–0.80)0.76 (0.71–0.82)0.38 (0.24–0.58)4.9 × 10−170.57
rs2660753 3/UnknownG/A 871106740.101.12 (1.06–1.18)1.12 (1.06–1.19)1.32 (1.09–1.61)1.2 × 10−50.73
rs17021918 4/PDLIM5G/A 955628770.350.88 (0.85–0.91)0.86 (0.83–0.90)0.80 (0.74–0.85)6.7 × 10−150.39
rs12500426 4/PDLIM5G/T 955146090.461.10 (1.06–1.13)1.11 (1.06–1.18)1.20 (1.12–1.28)4.8 × 10−80.54
rs7679673 4/TET2C/A 1060615340.400.88 (0.85–0.90)0.87 (0.83–0.91)0.77 (0.72–0.82)1.0 × 10−160.08
rs9364554 6/SLC22A3C/T 1608336640.291.10 (1.06–1.14)1.12 (1.07–1.18)1.18 (1.09–1.27)4.8 × 10−80.85
rs10486567 7/JAZF1G/A 279765630.230.85 (0.82–0.89)0.86 (0.81–0.91)0.72 (0.63–0.81)4.5 × 10−120.21
rs6465657 7/LMTK2A/G 978163270.461.10 (1.06–1.13)1.09 (1.04–1.15)1.21 (1.13–1.28)3.4 × 10−90.32
rs1447295 8/UnknownG/T 1284850380.111.41 (1.35–1.48)1.41 (1.34–1.49)2.01 (1.69–2.41)1.4 × 10−460.50
rs6983267 8/UnknownC/A 1284133050.490.82 (0.79–0.85)0.80 (0.76–0.85)0.67 (0.63–0.72)2.3 × 10−350.61
rs16901979 8/UnknownG/T 1281249160.031.56 (1.44–1.68)1.55 (1.43–1.69)2.39 (1.47–3.86)3.8 × 10−280.29
rs2928679 8/SLC25A37C/T 234389750.481.04 (1.01–1.07)1.03 (.97–1.09)1.08 (1.01–1.16)0.020.10
rs1512268 8/NKX3.1G/A 235264630.431.13 (1.10–1.17)1.13 (1.08–1.19)1.29 (1.21–1.37)2.6 × 10−160.19
rs4962416 10/CTBP2A/G 1266968720.281.04 (1.01–1.08)1.03 (0.98–1.08)1.11 (1.02–1.21)0.020.68
rs10993994 10/MSMBG/A 515494960.391.24 (1.20–1.28)1.21 (1.15–1.27)1.56 (1.46–1.66)7.9 × 10−410.36
rs7931342 11/UnknownC/A 689944970.500.84 (0.81–0.86)0.86 (0.82–0.91)0.70 (0.65–0.74)4.8 × 10−270.86
rs7127900 11/UnknownG/A 22335740.191.23 (1.18–1.28)1.24 (1.18–1.30)1.47 (1.32–1.65)6.3 × 10−260.63
rs4430796 17/HNF1BA/G 360980400.480.81 (0.79–0.84)0.81 (0.77–0.85)0.66 (0.62–0.71)2.7 × 10−380.79
rs11649743 17/HNF1BG/A 360749790.190.88 (0.85–0.92)0.88 (0.83–0.92)0.79 (0.70–0.90)5.6 × 10−100.25
rs1859962 17/UnknownT/G 691087530.481.17 (1.14–1.21)1.22 (1.15–1.28)1.38 (1.30–1.47)3.7 × 10−240.19
rs2735839 19/KLK2/KLK3G/A 513646230.150.81 (0.77–0.85)0.82 (0.78–0.86)0.62 (0.53–0.73)1.1 × 10−190.06
rs5759167 22/BIL/TTLL1G/T 435002120.500.84 (0.82–0.87)0.83 (0.79–0.87)0.71 (0.67–0.76)3.4 × 10−280.87
rs5945619 X/NUDT11T/C 512416720.361.13 (1.10–1.16)1.28 (1.22–1.35)1.9 × 10−200.10
  • adbSNP rs number.

  • bMajor/minor allele, based on the frequencies in controls in PRACTICAL III data.

  • cBuild 37 position.

  • dMAF in controls in combined European dataset.

  • eOR (minor allele) from a logistic regression using all European samples stratified by studies with no adjustment.

  • fOR in heterozygotes, relative to major allele homozygotes.

  • gOR in minor allele homozygotes, relative to major allele homozygotes.

  • hCochran–Armitage test for trend.

  • iHeterogeneity P value among studies.