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.

From: Genome-wide association study of 1,5-anhydroglucitol identifies novel genetic loci linked to glucose metabolism

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

  1. *The association result with fasting glucose was extracted from the published MAGIC Consortium GWAS result11.
  2. §The gene closest to the variant and other candidate genes are listed (index gene).
  3. R2 information was calculated from the 1000 Genomes Project Phase 3 in European (EUR) population.
  4. #rs13229622 is an independent SNP with genome-wide significant association with 1,5-AG found through conditional analysis.
  5. 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.
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