Table 2.
Skull shape QTL (SSH.qtl) identified in this study.
| Shape QTL | Closest marker | Chr | Pos (cM) | LOD | Lower CI (bp) | Upper CI (bp) | Candidate CF genes |
|---|---|---|---|---|---|---|---|
| SSH.qtl1 | mCV24784983 | 1 | 10.5 | 12 | 5,920,984 | 25,974,921 | [Col9a1; Eya1] |
| SSH.qtl2 | rs3678634 | 1 | 52.6 | 28.3 | 115,819,089 | 127,021,793 | Fcgr2b [Gli2] |
| SSH.qtl3 | rs13466711 | 1 | 78.6 | 17.7 | 168,066,210 | 175,710,316 | |
| SSH.qtl4 | rs13480734 | 10 | 52.9 | 18.3 | 89,335,908 | 105,325,377 | [Alx1] |
| SSH.qtl5 | rs13481127 | 11 | 48.5 | 27.3 | 80,139,712 | 81,911,051 | |
| SSH.qtl6 | rs3672597 | 11 | 77.5 | 24.8 | 112,611,769 | 114,027,932 | [Sox9] |
| SSH.qtl7 | rs3717860 | 12 | 8.8 | 32.5 | 16,866,101 | 28,237,591 | Taf1b |
| SSH.qtl8 | rs3710348 | 13 | 13.4 | 19.5 | 30,941,216 | 35,713,142 | Itga2 |
| SSH.qtl9 | gnf13.115.241 | 13 | 62.8 | 13.4 | 110,281,304 | 118,066,332 | |
| SSH.qtl10 | rs6396829 | 14 | 20.1 | 28.1 | 30,970,692 | 38,186,621 | |
| SSH.qtl11 | CEL-15_43206205 | 15 | 16.8 | 15 | 39,391,647 | 47,392,759 | |
| SSH.qtl12 | rs4191367 | 16 | 35.4 | 13.9 | 54,657,678 | 66,961,706 | Epha3 [Arhgap31] |
| SSH.qtl13 | rs6298471 | 17 | 19.2 | 23.8 | 36,252,692 | 43,916,321 | |
| SSH.qtl14 | rs6328845 | 18 | 31.3 | 11.4 | 56,230,871 | 70,306,352 | PPargc1b [Slc26a2; Tcof1] |
| SSH.qtl15 | rs3023496 | 19 | 40.1 | 17 | 46,867,039 | 49,396,956 | |
| SSH.qtl16 | rs13476580 | 2 | 44.3 | 20.6 | 72,637,926 | 76,844,869 | |
| SSH.qtl17 | rs6209325 | 2 | 73.3 | 16.5 | 146,817,118 | 155,755,548 | Pax1; Cd93 [Asxl1] |
| SSH.qtl18 | rs6246699 | 3 | 18 | 14.6 | 34,942,416 | 39,449,337 | |
| SSH.qtl19 | rs4138887 | 3 | 44 | 13.4 | 96,754,992 | 130,100,724 | [Alx3;Col11a1;Gnai3] |
| SSH.qtl20 | rs3660863 | 4 | 3.1 | 9.7 | 3,867,296 | 11,352,972 | [Plag1; Chd7; Gdf6] |
| SSH.qtl21 | rs3711477 | 4 | 40.1 | 20.5 | 81,877,569 | 105,794,559 | [Frem1] |
| SSH.qtl22 | rs3663950 | 4 | 65.1 | 23.2 | 126,198,546 | 134,724,460 | Thrap3; Col16a1 [Arid1a] |
| SSH.qtl23 | rs13459085 | 5 | 17.3 | 24.8 | 20,284,721 | 35,523,469 | Cad; Whsc1 [Fgfr3; Shh; Hmx1; Sh3bp2] |
| SSH.qtl24 | CEL-5_117374791 | 5 | 59.3 | 14.7 | 117,729,579 | 119,888,175 | Tbx3 |
| SSH.qtl25 | rs6181382 | 6 | 35.5 | 34.8 | 78,232,602 | 84,781,463 | Dok1; Gcfc2 |
| SSH.qtl26 | rs6265387 | 6 | 78.2 | 27.3 | 144,446,852 | 148,260,112 | Arntl2 |
| SSH.qtl27 | rs13479395 | 7 | 49.5 | 16.4 | 78,470,627 | 90,617,547 | Kif7 |
| SSH.qtl28 | rs13479776 | 8 | 29.7 | 23.2 | 47,753,313 | 78,304,228 | |
| SSH.qtl29 | rs3714664 | 9 | 22.5 | 11.3 | 39,523,343 | 46,544,750 | [Pvrl1] |
| SSH.qtl30 | rs13480351 | 9 | 49.5 | 16 | 90,683,187 | 99,809,852 | [Foxl2] |
Fields are same as Table 1. Genes from our list of known craniofacial genes are given in square brackets. High priority candidates genes identified in this study for their potential involvement in craniofacial development are reported in boldface.