Table 2 SNP quality assessment statistics for the 22 markers assessed in the replication phase.

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

Chr

SNP

Ref/Alt Allele, Traitmodel

Discovery

Replication

EAF

Genotype

O(HET)

E(HET)

p-value

EAF

Genotype

O(HET)

E(HET)

p-value

1

rs1002487

T/C, FPG, HbA1C#

0.0594

5/151/1196

0.1117

0.112

0.8088

0.05119

5/110/1057

0.09386

0.0972

0.2241

2

rs4143782

C/T, FPG@

0.1812

47/396/909

0.1117

0.112

0.8088

0.1702

35/330/811

0.2803

0.2824

0.7791

3

rs12488539&

G/T, FPG@

0.2914

110/565/672

0.2929

0.2967

0.6466

0.2047

0/481/695

0.4094

0.3256

1.26E-16&

3

rs6762914&

T/C, FPG@

0.3197

135/595/623

0.4195

0.413

0.5978

0.205

0/482/694

0.4101

0.326

5.5E-11&

3

rs487321

A/G, FPG#

0.0821

8/206/1138

0.1524

0.1507

0.8567

0.0564

7/118/1048

0.1004

0.1066

0.0414

5

rs17065898

T/C, FPG@

0.1949

55/413/874

0.4398

0.435

0.708

0.0959

14/201/961

0.1709

0.1756

0.292

6

rs707927

A/G, FPG@

0.1062

15/257/1079

0.3077

0.3138

0.4864

0.1014

22/193/958

0.1649

0.1823

0.0121

6

rs1145784

G/A, FPG#

0.0983

12/242/1099

0.1902

0.1899

1

0.09617

16/194/965

0.1651

0.1738

0.09178

7

rs2522219

A/G, FPG#

0.04922

4/125/1222

0.1789

0.1773

0.8781

0.03712

0/87/1085

0.07423

0.0715

0.4022

8

rs1199028&

A/C, FPG#

0.1478

28/342/976

0.09252

0.0936

0.5619

0.1943

58/238/615

0.2613

0.3131

2.3E-06&

8

rs2599723

G/A, FPG#

0.0518

4/132/1214

0.09778

0.09833

0.7794

0.0627

7/134/1032

0.1144

0.1176

0.262

10

rs3812689

G/A, FPG#

0.06135

10/146/1197

0.2541

0.252

0.8291

0.0664

6/144/1024

0.1227

0.1241

0.6371

11

rs918988

T/C, FPG@

0.4217

256/629/468

0.4649

0.4877

0.0842

0.3236

165/598/671

0.417

0.4377

0.0855

11

rs1151501

A/G, FPG@

0.1116

16/270/1067

0.1996

0.1983

0.8917

0.0889

15/179/979

0.1527

0.162

0.0339

12

rs11179003

C/T, FPG#

0.0565

9/135/1209

0.0997

0.1067

0.0342

0.03731

3/101/1330

0.0704

0.0718

0.4451

13

rs7329697&

T/C, FPG#

0.09904

13/242/1098

0.1789

0.1785

1

0.113

41/184/951

0.1565

0.2005

5.2E-09&

13

rs4646213

G/A, FPG#

0.09202

12/225/1116

0.1663

0.1671

0.8702

0.09327

11/197/966

0.1678

0.1691

0.7305

14

rs3784240

G/A, FPG#

0.06615

11/157/1185

0.116

0.1235

0.04233

0.05641

6/120/1044

0.1026

0.1065

0.2609

15

rs1256826

A/G, FPG@

0.1135

20/267/1066

0.1973

0.2012

0.498

0.1213

22/240/909

0.205

0.2131

0.2151

17

rs930514

A/G, FPG@

0.4933

331/671/349

0.4967

0.4999

0.8277

0.4801

271/581/321

0.4944

0.4992

0.7114

17

rs12600570

C/T, FPG@

0.1482

34/333/986

0.2461

0.2525

0.3341

0.1444

28/358/1048

0.2497

0.247

0.7491

18

rs9959376

C/T, FPG#

0.09726

20/223/1109

0.1649

0.1756

0.02979

0.0966

18/191/967

0.1625

0.1745

0.0142

  1. #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.
  2. &The markers (rs12488539, rs6762914, rs1199028 and rs7329697) fail in HWE test in replication phase.
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