Table 3 List of the four identified risk variants associated with FPG either at genome-wide significant p-values (<1.8E-08) or at nominal p-values of 1.0 < E-06.

From: Genome-wide association study identifies novel risk variants from RPS6KA1, CADPS, VARS, and DHX58 for fasting plasma glucose in Arab population

SNP: Effect Allele: Trait

Gene: functional consequences

Phase

Effect SizeR

P-valueR

Effect SizeDM

P-valueDM

rs1002487: C#, FPG

RPS6KA1: intronic

Discovery

8.315

1.64E-08

8.297

1.58E-08

Replication

3.442

3.7E-04

3.509

2.15E-04

Meta

6.551

5.72E-11

6.652

2.89E-11

rs487321: A#, FPG

CADPS: intronic

Discovery

6.133

1.53E-07

6.161

1.23E-07

Replication

3.955

2.25E-06

3.88

3.033E-06

Meta

7.047

1.83E-12

7.031

2.054E-12

rs707927: G@,$, FPG

VARS, VWA7: intron in VARS, 2 Kb upstream of VWA7

Discovery

0.9453

8.24E-06

0.9262

1.19E-05

Replication

0.6375

8.25E-05

0.6503

3.18E-05

Meta

5.928

3.074E-09

6.033

1.61E-09

rs12600570: T@, FPG

DHX58: intronic

Discovery

0.8166

7.49E-06

0.8374

4.11E-06

Replication

0.3892

4.67E-03

0.3682

5.65E-03

Meta

5.142

2.715E-07

5.186

2.15E-07

The following associations with HbA1c are shown in this table for the sake of completion; HbA1c associations are not considered significant except in the case of RPS6KA1.

rs1002487: C#, HbA1C

RPS6KA1: intronic

Discovery

7.367

4.91E-08

7.186

9.649E-08

Replication

1.811

2.71E-03

1.875

0.00115

Meta

5.784

7.27E-09

5.896

3.71E-09

rs487321: A#, HbA1C

CADPS: intronic

Discovery

2.387

2.47E-03

2.38

2.44E-03

Replication

1.893

2.77E-04

1.826

3.82E-04

Meta

4.723

2.32E-06

4.569

3.18E-06

rs707927: G@, HbA1C

VARS, VWA7: intron in VARS, 2 Kb upstream of VWA7

Discovery

0.5632

5.43E-04

0.5502

6.96E-04

Replication

0.3689

1.63E-04

0.3799

8.33E-05

Meta

5.088

3.61E-07

5.181

2.21E-07

rs12600570: T@, HbA1C

DHX58: intronic

Discovery

0.31

2.82E-02

0.3344

1.76E-02

Replication

0.194

1.98E-02

0.1805

2.81E-02

Meta

3.179

1.47E-03

3.178

1.48E-03

  1. EffectSize, Effect size represents beta value for discovery and replication phases, and Z-score for meta-analysis. R-regular correction: Corrected for age, sex and the top 10 principal components that resulted from the Principal Components Analysis of the genotype data; DM: Corrected for diabetes medication in addition to the regular correction.
  2. #association with the trait was observed under the genetic model based on recessive mode of inheritance; @association with the trait was observed under the genetic model based on additive mode of inheritance.
  3. $Upon performing inverse normal transformation on the FPG values, the p-values for association of the marker rs707927 with FPG improved in the discovery phase; the values were (p-value = 1.26E-07; effect size = 0.3314) which upon further correction for diabetes medication were (p-value = 2.72E-07; effect size = 0.3226).
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