Table 7.
ROH regions overlaying the identified risk variants.
| 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 |
@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.