Table 2.
Association of SNPs with HDL-C in Pima Indians from the Gila River Indian community
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| SNP ID | Locusa | Alleles |
HDL-C levels |
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| R/NR | RAF | Full Pima (n=2,717) | Non-full Pima (n=2,777) |
Combined (n=5,494) | |||||
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| Effect (%)b |
p value | Effect (%)b |
p value | Effect (%)b |
p value | ||||
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| rs17231506 | CETP | C/T | 0.65 | −6.9 | 2.6×1018 | −6.2 | 6.7×10−16 | −6.6 | 2.6×10−32 |
| rs12720922 | CETP | A/G | 0.30 | −6.4 | 1.9×10−17 | −6.8 | 4.2×10−17 | −6.5 | 3.1×10−32 |
| rs56322906 | DOCK6 | A/G | 0.46 | −3.3 | 2.8×10−5 | −3.5 | 4.2×10−6 | −3.5 | 1.4×10−10 |
| rs9987289 | PPP1R3B | A/G | 0.26 | −3.4 | 7.5×10−5 | −3.3 | 4.9×10−5 | −3.4 | 6.2×10−9 |
| rs1883025 | ABCA1 | T/C | 0.37 | −3.0 | 1.7×10−4 | −3.3 | 2.0×10−5 | −3.1 | 1.2×10−8 |
| rs1532085 | LIPC | G/A | 0.62 | −1.8 | 0.02 | −3.2 | 1.2×10−5 | −2.6 | 2.3×10−6 |
| rs838880 | SCARB1 | T/C | 0.59 | −1.8 | 0.02 | −2.7 | 2.6×10−4 | −2.3 | 2.0×10−5 |
| rs4731702 | KLF14 | C/T | 0.43 | −2.5 | 2.8×10−3 | −1.5 | 0.05 | −2.0 | 4.4×10−4 |
| rs7134594 | MMAB | C/T | 0.70 | −2.5 | 4.6×10−3 | −1.3 | 0.10 | −1.9 | 1.4×10−3 |
| rs1077834 | LIPC | A/G | 0.20 | −2.9 | 0.01 | −1.6 | 0.09 | −2.1 | 3.9×10−3 |
| rs10127775 | GALNT2 | A/T | 0.41 | −1.8 | 0.02 | −0.9 | 0.28 | −1.3 | 0.02 |
| rs1800961 | HNF4A | T/C | 0.03 | −6.5 | 7.3×10−3 | −0.7 | 0.71 | −3.1 | 0.05 |
Association with HDL-C was analysed in full-heritage Pima Indians, non-full-heritage Pima Indians and in the combined dataset. Natural logarithm of HDL-C was analysed, and the regression coefficient was exponentiated to obtain the effect estimate, expressed as a multiplier
a
Locus is based on previously reported data [7], where ever possible a plausible candidate gene is listed
b
Effect is given as percentage reduction in HDL-C level per copy of the risk allele
NR, non-risk allele; R, risk allele (HDL-C lowering allele); RAF, risk allele frequency in Pima Indians