TABLE 2

Replication of 13 100K SNP associations within FHS

SNPGeneLocation (hg18)StrandAllelesMAF (allele)100K FHS family set (n = 1,087)
FHS unrelated replication (n = 1,465)
DM HR (95% CI)*Cox P (BMI)FBAT P (BMI)TraitAlleleGEE P (BMI)FBAT P (BMI)DM HR (95% CI)*Cox PAlleleRegression P
rs625643AK024684chr1:54409755A/G0.25 (A)1.06 (0.73–1.50)0.77 (0.86)0.36 (0.34)Fasting insulinG0.009 (0.08)0.44 (0.32)1.39 (1.0–1.80)0.02G0.006
AK122760FPGG0.004 (0.03)0.03 (0.03)G0.73
ISI_0–120A0.005 (0.02)0.90 (0.66)G0.87
HOMA-IRG0.0008 (0.01)0.13 (0.06)G0.03
mFPGG0.006 (0.03)0.04 (0.07)G0.15
rs952635PDE4Bchr1:66464473A/G0.31 (G)0.56 (0.40–0.79)0.0007 (0.003)0.16 (0.12)FPGA0.0004 (0.006)0.02 (0.01)0.89 (0.69–1.10)0.34A0.03
ISI_0–120G0.003 (0.02)0.18 (0.08)G0.17
A1CA0.003 (0.008)0.30 (0.21)A0.75
HOMA-IRA0.004 (0.051)0.40 (0.20)A0.048
mFPGA0.0003 (0.002)0.03 (0.02)A0.36
rs7531174SLC44A3chr1:95110679C/T0.21 (C)0.58 (0.42–0.80)0.0009 (0.0002)0.09 (0.07)FPGC0.006 (0.005)0.34 (0.41)0.84 (0.65–1.10)0.20C0.31
A1CC0.0002 (0.0002)0.005 (0.01)C0.02
mFPGC0.0009 (0.001)0.39 (0.47)C0.58
rs1489100AJ012503chr3:76215254A/G0.41 (G)0.75 (0.54–1.0)0.09 (0.18)0.001 (0.002)FPGA0.051 (0.09)0.003 (0.004)0.72 (0.57–0.91)0.007A0.11
A1CA0.0007 (0.001)0.006 (0.01)A0.38
mFPGA0.09 (0.12)0.003 (0.005)A0.13
rs2715755MORC1chr3:110164908C/T0.39 (C)1.22 (0.86–1.70)0.27 (0.10)0.01 (0.02)Fasting insulinT0.29 (0.33)0.003 (0.02)0.98 (0.78–1.20)0.88T0.70
ISI_0–120C0.10 (0.10)0.006 (0.04)C0.01
HOMA-IRT0.20 (0.24)0.003 (0.03)T0.60
rs729511SLC9A9chr3:144538397+A/G0.44 (A)1.43 (1.0–2.0)0.03 (0.03)0.008 (0.006)Fasting insulinG0.002 (0.046)0.31 (0.70)1.12 (0.90–1.40)0.32G0.02
ISI_0–120A0.002 (0.01)0.054 (0.058)A0.75
HOMA-IRG0.004 (0.07)0.14 (0.31)G0.02
rs2545523Gene desertchr5:165446786A/T0.20 (T)0.95 (0.64–1.40)0.80 (0.66)0.52 (0.33)Fasting insulinT0.002 (0.006)0.75 (0.77)1.21 (0.94–1.60)0.13T0.07
CNCISI_0–120A0.01 (0.03)0.002 (0.003)A0.07
HOMA-IRT0.007 (0.02)0.64 (0.89)T0.04
rs1355037ZPBPchr7:50063624+C/G0.23 (C)0.84 (0.61–1.20)0.32 (0.58)0.006 (0.045)Fasting insulinC0.02 (0.33)0.0003 (0.04)0.94 (0.72–1.20)0.67C0.61
ISI_0–120G0.40 (0.95)0.01 (0.09)G0.006
HOMA-IRC0.04 (0.48)0.001 (0.10)C0.86
rs1416406(SORCS1)chr10:109034861C/T0.27 (T)1.21 (0.88–1.70)0.23 (0.31)0.38 (0.62)Fasting insulinT0.003 (0.01)0.06 (0.29)1.22 (0.97–1.50)0.094T0.07
120 kbISI_0–120C0.006 (0.02)0.005 (0.02)C0.14
HOMA-IRT0.001 (0.005)0.01 (0.07)T0.04
rs10500679(HNRNPGT)chr11:7112939C/G0.28 (C)0.82 (0.60–1.10)0.20 (0.28)0.66 (0.53)Fasting insulinC0.002 (0.009)0.57 (0.77)1.25 (0.96–1.60)0.10C0.83
44 kbISI_0–120G0.004 (0.004)0.59 (0.75)G0.31
A1CG0.25 (0.16)0.001 (0.0004)G0.03
HOMA-IRC0.0008 (0.003)0.73 (0.97)C0.91
rs2806739Gene desertchr13:53199780+C/T0.22 (T)1.31 (0.91–1.90)0.14 (0.12)0.045 (0.055)FPGT0.006 (0.005)0.004 (0.01)1.51 (1.20–1.90)0.001T0.26
CNCISI_0–120C0.09 (0.07)0.0006 (0.001)T0.77
HOMA-IRT0.08 (0.04)0.003 (0.009)T0.53
mFPGT0.003 (0.0008)0.03 (0.02)T0.27
rs2241119TSHRchr14:80628718C/T0.12 (C)1.99 (1.10–3.50)0.02 (0.01)0.44 (0.21)FPGT0.0005 (0.003)0.09 (0.10)1.02 (0.73–1.40)0.92T0.27
A1CT0.001 (0.004)0.13 (0.08)C0.77
HOMA-IRT0.0008 (0.003)0.02 (0.009)T0.046
mFPGT0.00004 (0.0003)0.09 (0.09)T0.07
rs2009833ATP8B4chr15:47980845+A/G0.35 (A)0.77 (0.56–1.10)0.10 (0.18)0.02 (0.03)FPGA0.06 (0.04)0.005 (0.02)0.79 (0.63–0.99)0.037A0.001
A1CA0.02 (0.006)0.004 (0.004)A0.001
HOMA-IRA0.07 (0.02)0.006 (0.003)A0.04
mFPGA0.08 (0.03)0.005 (0.003)A0.002
  • Association of SNPs selected by the multiple related trait strategy with diabetes and/or quantitative traits in the FHS 100K family sample and replication in the nonoverlapping FHS unrelated sample. If the SNP lies within a gene, the gene (italics) or mRNA (no italics) is indicated; if not, the nearest gene is shown in parentheses, with distance in kilobase pairs below the gene name. SNPs located >400 kb from a known gene or mRNA are considered to be in a gene desert; those labeled “CNC” reflect proximity to a conserved noncoding region. The strand on which the SNP was genotyped is stated. Alleles are shown in alphabetical order, with the minor allele in parentheses next to the MAF in FHS, and the HR (*) calculated as second allele versus first allele. The allele associated with the higher level of each trait is shown to the right of the trait. The P values in parentheses indicate adjustment for BMI. Chr, chromosome.