Table 2.
CNV associations in gene regions previously identified by SNP GWAS
| SNP GWAS | Gene | Association | Phenotype | p valuea | p value (SNP study) | With SNPb | |
|---|---|---|---|---|---|---|---|
| Cole et al.1,4 | DPP6 | reported SNP | rs114189713 | mouth width | 7.26 × 10−8 | 1.87 × 10−7 | 0.067 |
| CNV region | 7: 153,860,000–153,870,000 | lower lip height | 2.93 × 10−3 | ||||
| lower facial depth (average) | 1.78 × 10−2 | ||||||
| Claes et al.2 | HOXD@ | Reported SNP | rs970797 | nose width; mouth and philtrum | 5.47 × 10−1 | 6.17 × 10−11 | 0.254 |
| CNV region | 2: 176,918,000–176,977,000 | head circumference | 1.93 × 10−3 | ||||
| lower facial height | 4.64 × 10−3 | ||||||
| nasal width | 7.58 × 10−3 | ||||||
| inner canthal width | 9.02 × 10−3 | ||||||
| PC5 | 2.45 × 10−2 | ||||||
| White et al.3c | FGFRL1 | Reported SNP | rs74921869 | quadrant 2: region of the nose | 8.95 × 10−1 | 3.51 × 10−11 | 0.0002 |
| CNV region | 4: 931,000–1,060,000 | centroid size | 2.20 × 10−2 | ||||
| PC5 | 3.87 × 10−2 | ||||||
| philtrum length | 2.44 × 10−2 | ||||||
| nasal width | 3.89 × 10−2 |
a
p value calculated with our sample. Due to CNV QC, our sample is slightly different than that of Cole et al.
b
Maximum SNP-window pairwise r2 within the region for the reported SNP.
c
Analysis windows with p values < 0.05 reported. Other two were reported for <2.5 × 10−2.