TABLE 4

Attempt at replication of 13 FHS genetic associations in external GWA datasets

SNPMexican Americans
Pima Indian case-control
Pima Indian sibs
Amish
DGI SNPr2DGI OR (95% CI)DGI OR P valueDGI QTDGI QT P value
ORPORPORPORP
rs6256430.700.321.510.210.330.181.110.36Same1.01.12 (0.97–1.29)0.12FPG0.17
T vs. CHOMA-IR0.21
rs9526350.840.541.120.371.160.460.890.33rs66646180.601.03 (0.91–1.18)0.60FPG0.04 (G)
T vs. GHOMA-IR0.057 (G)
rs75311740.850.630.940.621.000.981.000.99rs125651500.790.98 (0.84–1.14)0.75FPG0.57
A vs. THOMA-IR0.86
rs14891000.890.710.800.091.040.871.130.28rs76200011.00.92 (0.81–1.04)0.53FPG0.55
T vs. GHOMA-IR0.67
rs27157551.410.34Low MAFLow MAF1.230.08Same1.01.0 (0.88–1.14)0.91HOMA-IR0.49
G vs. A
rs7295110.890.671.240.090.760.161.010.96Same1.00.96 (0.85–1.09)0.79HOMA-IR0.47
A vs. G
rs25455230.991.001.070.591.100.630.960.76Same1.01.02 (0.88–1.18)0.91HOMA-IR0.86
A vs. T
rs13550370.991.000.990.960.820.330.830.21Same1.01.05 (0.91–1.21)0.82HOMA-IR0.55
C vs. G
rs14164060.820.520.990.920.920.651.070.59rs107870191.00.95 (0.83–1.09)0.40HOMA-IR0.37
T vs. G
rs105006792.190.02Low MAFLow MAF1.020.87rs172812320.921.01 (0.86–1.19)0.98FPG0.68
T vs. CHOMA-IR0.004 (T)
rs28067391.060.890.750.0520.860.491.220.11rs42429320.870.91 (0.78–1.06)0.08FPG0.93
T vs. GHOMA-IR0.63
rs22411191.100.850.800.180.910.711.020.90Same1.01.18 (1.0–1.41)0.19FPG0.52
G vs. AHOMA-IR0.75
rs20098330.670.160.880.521.400.320.900.31rs80238090.391.07 (0.92–1.24)0.69FPG0.74
A vs. GHOMA-IR0.37
  • The 100K FHS SNPs that showed replication in a nonoverlapping unrelated FHS cohort (Table 2) were examined for association with diabetes in three other 100K datasets, and for replication of their association with diabetes, FPG or HOMA-IR in the 500K DGI dataset; please see their respective publications for a description the statistical methods of each study. DGI data were obtained from http://www.broad.mit.edu/diabetes/ (March 2007). SNPs that did not meet MAF thresholds in the Pima Indian case-control or sib datasets were not analyzed. If the FHS SNP was not present in the 500K DGI array, the SNP in strongest linkage disequilibrium (as measured by r2 using data from phase 2 of the HapMap in the CEU population) was examined. In the DGI, the associated alleles are indicated below the OR or, for relevant quantitative traits (QT), next to the corresponding P value. Nominally significant associations are shown in boldface.