Table 6 Results from the analysis of examining the identified associations in sub-cohorts of entirely diabetic patients or of entirely healthy participants.

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 SizeBMI+LM

P-valueBMI+LM

Effect SizeBMI+LM+DM

P-valueBMI+LM+DM

rs1002487: C#, FPG

RPS6KA1: intronic

Discovery_diabetic

6.396

2.48E-04

6.487

2.11E-04

6.488

2.12E-04

Discovery_non- diabetic&

NA

NA

NA

NA

  

Replication_diabetic

17.83

4.74E-07

17.72

6.07E-07

17.7

6.50E-07

Replication_non- diabetic

0.0086

0.9886

−0.08115

0.8861

  

Meta_diabetic

6.011

1.84E-09

6.014

1.81E-09

6.004

1.93E-09

Meta_non-diabetic

0.014

0.9886

0.143

0.8861

  

Meta_all

4.173

3.0E-05

4.062

4.86E-05

  

rs487321: A#, FPG

CADPS: intronic

Discovery_diabetic

5.781

3.1E-04

5.799

3.1E-04

5.797

3.1E-04

Discovery_non- diabetic

−0.117

0.9872

0.1009

0.8885

  

Replication_diabetic

9.392

2.1E-04

9.346

2.36E-04

9.594

1.84E-04

Replication_non- diabetic

2.479

4.64E-08

2.429

1.07E-08

  

Meta_diabetic

5.132

2.86E-07

5.116

3.12E-07

5.154

2.55E-07

Meta_non-diabetic

4.190

2.78E-05

4.486

7.27E-06

  

Meta_all

6.420

1.36E-10

6.648

2.97E-11

  

rs707927: G@, FPG

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

Discovery_diabetic

1.153

1.50E-03

1.157

1.51E-03

1.155

1.54E-03

Discovery_non- diabetic

0.1979

3.3E-02

0.1858

4.18E-02

  

Replication_diabetic

1.516

4.23E-04

1.518

4.35E-04

1.517

4.47E-04

Replication_non- diabetic

0.2364

1.1E-02

0.2011

2.04E-02

  

Meta_diabetic

4.683

2.83E-06

4.677

2.91E-06

4.668

3.05E-06

Meta_non-diabetic

3.327

8.78E-04

3.083

2.05E-03

  

Meta_all

5.458

4.82E-08

5.259

1.45E-07

  

rs12600570: T@, FPG

DHX58: intronic

Discovery_diabetic

0.8421

8.46E-03

0.8328

9.55E-03

0.8303

9.85E-03

Discovery_non- diabetic

0.2308

3.35E-03

0.217

5.21E-03

  

Replication_diabetic

0.5816

0.101

0.5767

0.1052

0.5874

0.1002

Replication_non- diabetic

0.1955

1.2E-02

0.1955

1.17E-02

  

Meta_diabetic

3.080

2.07E-03

3.035

2.4E-03

3.042

2.35E-03

Meta_non-diabetic

3.814

1.30E-04

3.724

1.96E-04

  

Meta_all

4.898

9.71E-07

4.799

1.59E-06

  
  1. &In the case of the RPS6KA1 marker, all the individuals with genotype homozygous for risk allele were seen with the sub-cohort of Discovery_diabetic) and hence results for Discovery_ non-diabetic sub-cohort were unavailable.
  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. EffectSizeEffect size represents beta value for discovery and replication phases, and Z-score for meta-analysis. RRegular correction - Corrected for age, sex and the top 10 principal components that resulted from the Principal Components Analysis of the genotype data; BMI+LMCorrected for BMI and lipid medication in addition to the regular correction; BMI+LM+DMCorrected for BMI and lipid & diabetes medications in addition to the regular correction.
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