TABLE 1

Allele frequencies and evidence for association in case and control study samples for SNPs in the HNF4A region

kb position*SNP nameMajor/minor alleleMinor allele frequency (n typed)
P valueMultiplicative OR (95% CI)
F1F2F1 + F2Control
−9.422rs4810424§G/C0.20 (530)0.20 (259)0.20 (789)0.16 (409)0.0141.32 (1.05–1.64)
−4.030rs1884613C/G0.21 (526)0.21 (261)0.21 (787)0.16 (410)0.0101.34 (1.07–1.66)
−3.926rs1884614§C/T0.20 (516)0.20 (260)0.20 (776)0.16 (402)0.0171.31 (1.04–1.63)
1.272rs2144908G/A0.21 (530)0.21 (263)0.21 (793)0.16 (413)0.0111.33 (1.06–1.65)
5.269rs6031551T/C0.19 (527)0.18 (262)0.18 (789)0.22 (401)0.0300.79 (0.64–0.98)
5.349rs6031552C/A0.19 (527)0.18 (263)0.18 (790)0.23 (409)0.0150.77 (0.63–0.95)
39.604rs2425637G/T0.53 (528)0.52 (262)0.53 (790)0.47 (406)0.0141.23 (1.04–1.47)
43.592rs2425640G/A0.37 (525)0.34 (261)0.36 (786)0.41 (410)0.0210.82 (0.68–0.97)
44.840rs1800963C/A0.42 (529)0.44 (260)0.43 (789)0.45 (409)0.4480.93 (0.79–1.11)
50.693rs3212183T/C0.42 (515)0.43 (238)0.43 (753)0.38 (400)0.0401.20 (1.01–1.44)
54.595rs1885088G/A0.14 (531)0.16 (262)0.15 (793)0.11 (409)0.0171.37 (1.05–1.75)
66.316rs1028583§G/T0.43 (512)0.44 (263)0.43 (775)0.45 (392)0.3720.92 (0.78–1.10)
73.035rs3818247§G/T0.32 (522)0.32 (261)0.32 (783)0.34 (391)0.2360.89 (0.75–1.07)
  • *

    * Kilobase position from the HNF4A P2 promoter translation initiation site at chromosome 20, base position 43,669,874 of the human reference sequence (UCSC Genome Browser, July 2003);

  • calculated for F1 + F2 case vs. control subjects;

  • calculated for F1 + F2 case vs. control subjects for the minor allele in control;

  • §

    § SNPs originally tested for association by Love-Gregory et al. (23);

  • SNP associated with disease status in Ashkenazi sample (23). F1, FUSION 1; F2, FUSION 2.