Table 2.
The seven genome-wide significant index SNPs (p < 5 × 10−8) associated with 1,5-anhydroglucitol in 7,550 European American subjects from the ARIC study.
| Index SNP | Discovery GWAS (1,5-AG) | Reported Association with Fasting Glucose* | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Locus§ | Variant ID | A1/A2 | AF | Effect (SE), ug/mL | P | Expl Var (%) | Proxy SNP | R2 with index SNP¶ (D’) | Effect (SE), mmol/l | P |
| EFNA1/SLC50A1 | rs9330264 | T/C | 0.36 | 0.64 (0.10) | 2.96 × 10−10 | 0.51 | rs11264319 | 0.53 (0.96) | −0.0065 (0.0036) | 0.07 |
| MCM6/LCT | rs182549 | C/T | 0.33 | −1.19 (0.10) | 6.54 × 10−32 | 1.91 | rs4988235 | 1 (1) | −0.0015 (0.004) | 0.7 |
| SI | rs9825346 | G/A | 0.41 | −0.54 (0.10) | 1.28 × 10−8 | 0.42 | rs9825346 | 1 | 0.0038 (0.0038) | 0.32 |
| MGAM | rs11976181 | T/C | 0.17 | 1.11 (0.12) | 2.62 × 10−19 | 1.03 | rs3800993 | 1 (1) | −0.0078 (0.005) | 0.12 |
| MGAM2 | rs13229622# | C/G | 0.22 | −0.73 (0.11) | 8.64 × 10−11 | 0.54 | Not investigated due to lack of conditional estimates | |||
| SLC5A10 | rs117355297 | T/C | 0.04 | −2.13 (0.26) | 3.83 × 10−16 | 0.39 | rs1621499 | 0.28 (0.97) | 0.0043 (0.0055) | 0.43 |
| SLC5A1 | rs117086479 | G/A | 0.06 | −1.09 (0.20) | 4.05 × 10−8 | 0.87 | rs4821013 | 1 (1) | 0.019 (0.0073) | 0.0072 |
*The association result with fasting glucose was extracted from the published MAGIC Consortium GWAS result11.
§The gene closest to the variant and other candidate genes are listed (index gene).
¶R2 information was calculated from the 1000 Genomes Project Phase 3 in European (EUR) population.
#rs13229622 is an independent SNP with genome-wide significant association with 1,5-AG found through conditional analysis.
A1 is the effect allele, i.e. the allele for which effect estimates are provided. Abbreviations: AF = effect allele frequency; SE = standard error; Expl Var = proportion of 1,5-AG variance explained.