TABLE 5

SNPs associated with type 2 diabetes and/or related traits in FHS that show nominally significant associations in the DGI dataset

ChrSNPGenePositionFHS
DGI
Alleles (MAF)HR P (BMI)HR (95% CI)TraitQT GEE P (BMI)QT FBAT P (BMI)SNP on 500Kr2mType 2 diabetes P valueOR (95% CI)TraitPβ
1rs952635PDE4B64982242A/G0.00070.56FPG0.0004 (0.006)0.02 (0.01)rs66646180.60T0.601.03FPG0.04−0.08
0.310.003(0.40–0.79)HOMA-IR0.004 (0.051)0.40 (0.20)(0.91–1.18)HOMA-IR0.057−0.07
1rs963328FLVCR186263657A/C0.370.87FPG0.38 (0.60)0.25 (0.78)Same1.0G0.790.99FPG0.64−0.02
0.480.55(0.64–1.20)HOMA-IR0.30 (0.66)0.0003 (0.02)(0.87–1.12)HOMA-IR0.03−0.09
2rs385909LOC400937256807C/T0.110.71FPG0.0001 (0.002)0.07 (0.32)rs3896211.0T0.970.98FPG0.35−0.05
0.130.27(0.47–1.10)HOMA-IR0.00006 (0.0002)0.03 (0.20)(0.82–1.16)HOMA-IR0.04−0.11
2rs300703SH3YL1302047C/T0.081.54FPG0.0006 (0.008)0.12 (0.24)rs42413161.0C0.960.96FPG0.35−0.05
0.110.16(0.94–2.50)HOMA-IR0.00003 (0.0006)0.11 (0.20)(0.80–1.15)HOMA-IR0.046−0.11
2rs10497719(MYO1B)185972926C/T0.000032.03FPG0.04 (0.10)0.07 (0.07)rs173518031.0C0.161.09FPG0.010.15
0.110.004(1.50–2.80)HOMA-IR0.13 (0.18)0.22 (0.27)(0.91–1.32)HOMA-IR0.910.01
5rs10491394EFNA5102784623A/G0.020.58FPG0.001 (0.008)0.005 (0.007)Same1.0C0.470.94FPG0.01−0.12
0.180.06(0.37–0.90)HOMA-IR0.003 (0.02)0.02 (0.01)(0.80–1.11)HOMA-IR0.86−0.01
5rs1918159(BC045192)112977574C/G0.0020.56FPG0.002 (0.003)0.01 (0.02)rs171428891.0T0.631.07FPG0.040.12
0.140.007(0.39–0.81)HOMA-IR0.009 (0.03)0.04 (0.04)(0.89–1.30)HOMA-IR0.320.06
5rs1990930SIL1134614609A/G0.030.71FPG0.009 (0.02)0.03 (0.03)rs117446951.0G0.030.85FPG0.16−0.05
0.460.055(0.52–0.98)HOMA-IR0.02 (0.12)0.07 (0.0505)(0.75–0.97)HOMA-IR0.25−0.04
6rs10498861BC03131269343049A/G0.091.52FPG0.005 (0.07)0.03 (0.13)rs69398620.93T0.560.96FPG0.04−0.12
0.120.14(0.93–2.50)HOMA-IR0.0002 (0.04)0.049 (0.24)(0.79–1.16)HOMA-IR0.56−0.03
6rs6910169(BC036223)113625254C/T0.900.98FPG0.006 (0.04)0.00003 (0.0002)rs12991581.0C0.480.96FPG0.300.04
0.430.85(0.74–1.30)HOMA-IR0.06 (0.35)0.008 (0.02)(0.84–1.09)HOMA-IR0.04−0.08
7rs2024265NOM1155987004A/G0.0471.43FPG0.0007 (0.03)0.13 (0.38)rs102561841.0C0.0070.81FPG0.11−0.07
0.220.14(1.0–2.0)HOMA-IR0.16 (0.82)0.38 (0.87)(0.70–0.93)HOMA-IR0.56−0.03
10rs2025463SFMBT27199259C/T0.020.66FPG0.02 (0.03)0.15 (0.12)rs112550490.84T0.041.15FPG0.30−0.05
0.290.01(0.46–0.94)HOMA-IR0.03 (0.06)0.053 (0.03)(1.0–1.33)HOMA-IR0.28−0.05
10rs7089102(BC017976)51109048G/T0.0080.68FPG0.008 (0.01)0.86 (0.93)rs70826071.0G0.841.01FPG0.45−0.03
0.470.006(0.51–0.90)HOMA-IR0.001 (0.02)0.56 (0.93)(0.89–1.14)HOMA-IR0.020.09
10rs1591565(AK056904)79197636C/G0.860.97FPG0.33 (0.35)0.01 (0.003)Same1.0G0.331.06FPG0.620.02
0.330.86(0.72–1.30)HOMA-IR0.02 (0.02)0.001 (0.0004)(0.93–1.21)HOMA-IR0.0010.13
10rs10509927(SMC3)106203638A/G0.0541.5FPG0.03 (0.04)0.37 (0.61)rs49185730.70T0.611.05FPG0.220.06
0.130.059(1.0–2.30)HOMA-IR0.002 (0.003)0.13 (0.64)(0.89–1.23)HOMA-IR0.050.10
10rs10509928(SMC3)106203679G/T0.031.56FPG0.02 (0.03)0.35 (0.62)rs49185730.70T0.611.05FPG0.220.06
0.130.04(1.0–2.30)HOMA-IR0.001 (0.002)0.07 (0.50)(0.89–1.23)HOMA-IR0.050.10
10rs845080CR607950118930209A/G0.500.9FPG0.08 (0.09)0.009 (0.02)rs7051460.68T0.841.05FPG0.940
0.390.79(0.65–1.20)HOMA-IR0.11 (0.20)0.009 (0.02)(0.93–1.19)HOMA-IR0.030.08
11rs10500679HNRNPG-T7275478C/G0.200.82FPG0.05 (0.08)0.71 (0.65)rs172812320.92T0.981.01FPG0.680.02
0.280.28(0.60–1.10)HOMA-IR0.0008 (0.003)0.73 (0.97)(0.86–1.19)HOMA-IR0.0040.14
11rs1151488MAP3K1162698321C/T0.000050.54FPG0.02 (0.004)0.94 (0.61)Same1.0C0.121.09FPG0.940
0.320.00002(0.40–0.73)HOMA-IR0.17 (0.06)0.42 (0.11)(0.95–1.25)HOMA-IR0.030.09
11rs1387153LOC64748389978446C/T0.161.28FPG0.004 (0.01)0.13 (0.17)rs38475540.59T0.541.04FPG0.040.08
0.280.21(0.90–1.80)HOMA-IR0.07 (0.23)0.59 (0.91)(0.92–1.18)HOMA-IR0.970
12rs1730454LOC64306346532538A/G0.0470.54FPG0.01 (0.02)0.38 (0.56)rs20780330.95A0.951.02FPG0.05−0.11
0.120.046(0.29–1.0)HOMA-IR0.002 (0.0005)0.09 (0.10)(0.85–1.22)HOMA-IR0.18−0.07
12rs10506806SYT179121551C/T0.020.66FPG0.0003 (0.0009)0.0005 (0.0003)Same1.0T0.381.03FPG0.02−0.10
0.300.06(0.46–0.94)HOMA-IR0.03 (0.06)0.003 (0.002)(0.90–1.18)HOMA-IR0.35−0.04
13rs478243LATS22640558C/T0.080.77FPG0.01 (0.01)0.11 (0.11)Same1.0C0.571.05FPG0.86−0.01
0.340.049(0.58–1.0)HOMA-IR0.01 (0.02)0.003 (0.007)(0.91–1.21)HOMA-IR0.010.10
20rs6074234LOC33959311098703C/T0.00092.12FPG0.08 (0.18)0.91 (0.43)rs61311451.0T0.011.26FPG0.310.06
0.110.0008(1.40–3.30)HOMA-IR0.01 (0.06)0.59 (0.12)(1.05–1.51)HOMA-IR0.480.04
20rs4142363LOC33959311099044C/T0.00092.05FPG0.08 (0.15)0.87 (0.45)rs61311451.0T0.011.26FPG0.310.06
0.110.0009(1.30–3.10)HOMA-IR0.02 (0.06)0.49 (0.12)(1.05–1.51)HOMA-IR0.480.04
  • Of 763 SNPs selected for presumptive association with diabetes and/or related traits in the FHS 100K dataset, 25 SNPs examined by the DGI investigators (either the same SNPs or SNPs from the 500K Affymetrix array in linkage disequilibrium with the FHS 100K SNPs) showed consistent nominal associations with the same quantitative traits in the DGI. The degree of linkage disequilibrium is indicated by r2; DGI SNPs in bold served as proxies for more than one 100K SNP. In the FHS dataset, alleles are shown in alphabetical order with the minor allele in bold and the MAF below; HRs with 95% CI are estimated as second allele versus first allele. In FHS, quantitative trait (QT) P values are shown without and with adjustment for BMI (in parentheses). In the DGI, ORs are estimated as the minor allele versus the major allele: the minor allele (m) is shown. In the DGI, quantitative traits are estimated for the minor allele, with the direction of the effect indicated by the positive or negative sign of the β estimate. When alleles for the same SNP are not identical between both datasets, they were genotyped on opposite strands. The genes (italicized) or mRNAs (not italicized) in which SNPs lie are shown; otherwise, the nearest gene or mRNA is indicated in parentheses. DGI data were obtained from http://www.broad.mit.edu/diabetes/ (March 2007). Chr, chromosome.