Table 7 ROH regions overlaying the identified risk variants.

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

SNP

ROH group and the method used to identify the ROH@

Consensus ROH region

Distance to SNP from consensus ROH (in Mb)

Number of individuals from the discovery cohort (n = 1353) harboring the ROH (Distribution into sub-cohort of participants diagnosed for T2DM (n = 605) versus sub-cohort of non-diabetic participants (n = 748))

Length of consensus ROH (in Kb)

Count of SNPs in consensus ROH region

Mean ± SD of ROH groups

Distance to SNP from mean ± SD window (in Mb)

Presence of SNP in ROH regions identified in worldwide population (from Pemberton et al. study48)

rs1002487/RPS6KA1

S18181

1:28864435–29062427

1.99

51 (29:22)

197.99

11

24917436–33009426

Overlapping

Yes

S15572

1:28056342–28084571

1.19

44 (27:17)

28.23

5

27723540–28417372

0.85

rs487321/CADPS

S71771

3:62647115–63435226

0.143

29 (17:12)

788.11

226

3:55304385–70777955

Overlapping

Yes

S71761

3:62315312–62315312

0.475

29 (16:13)

0.001

1

3:55748124–68882499

Overlapping

S41142

3:61981197–62189189

0.60

31 (17:14)

207.99

85

3:56659352–67511033

Overlapping

S41152

3:62604010–62604010

0.186

31 (16:15)

0.001

1

3:57340271–67867749

Overlapping

S41162

3:62883050–63333375

0.0924

31 (18:13)

450.32

101

3:57761318–68455106

Overlapping

S41172

3:63663215–63670140

6.93

31 (18:13)

0.873

3

3:58212832–69120521

Overlapping

rs707927/[VARS, VWA7]

S17061

6:31001421–32989521

0.744

53 (29:24)

1988.10

1077

6:26827255–36745549

Overlapping

No, But LD SNP rs805267 (r2 = 0.69) is present

S6872

6:29569045–29593788

2.176

71 (38:33)

24.74

24

6:26617526–32545306

Overlapping

S8242

6:31872383–32161430

0.126

64 (34:30)

289.05

126

6:29115193–34918619

Overlapping

S10002

6:30112623–30125537

1.619

57 (30:27)

12.91

30

6:27129747–33108413

Overlapping

S10012

6:31572927–31572927

0.173

57 (31:26)

0.001

1

6:28490667–34655186

Overlapping

rs12600570/DHX58

S51531

17:39980819–40041676

Overlapping

34 (19:15)

60.858

8

17:36532212–43490282

Overlapping

No, But LD SNP rs2074158 (r2 = 0.56) is present

S17412

17:40041676–40063083

0.219

43 (22:21)

21.408

5

17:39559717–40545041

Overlapping

  1. @Two approaches were used to identify ROH segments (see Methods for details). Method 1: Markers that passed quality control were pruned for LD (r2 > 0.9) (n = 568,670) and employed to detect ROH segments using parameters suggested by Howrigan et al.52; Method 2: Un-pruned marker set (n = 632,375) was employed to detect ROH using parameters deployed in Christofidou et al.53.
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