Table 2.
SNP | Minor Allele | Minor allele frequency | All Clefts (n=494) | Cleft Lip/Palate (n=421) | Cleft Palate (n=73) | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
| ||||||||||||
Cases (n=494) | Controls (n=413) | P-value | Odds ratio | 95% CI | P-value | Odds ratio | 95% CI | P-value | Odds ratio | 95% CI | ||
MMP2 | ||||||||||||
rs243865 | T | 0.17 | 0.18 | 0.7534 | 0.96 | 0.75–1.23 | 0.9349 | 1.01 | 0.78–1.31 | 0.1115 | 0.66 | 0.40–1.10 |
rs2285053 | T | 0.13 | 0.15 | 0.2534 | 0.85 | 0.65–1.12 | 0.2577 | 0.85 | 0.63–1.13 | 0.4920 | 0.83 | 0.50–1.40 |
rs243847 | C | 0.36 | 0.37 | 0.8483 | 0.98 | 0.81–1.20 | 0.8652 | 1.02 | 0.83–1.25 | 0.3408 | 0.84 | 0.58–1.21 |
rs2287074 | A | 0.38 | 0.39 | 0.6948 | 0.96 | 0.79–1.16 | 0.7184 | 0.96 | 0.79–1.18 | 0.8303 | 0.96 | 0.67–1.37 |
rs9923304 | T | 0.37 | 0.37 | 0.8485 | 0.98 | 0.81–1.19 | 0.8040 | 0.97 | 0.79–1.20 | 0.9465 | 0.99 | 0.69–1.42 |
rs11639960 | G | 0.32 | 0.32 | 0.8882 | 0.99 | 0.81–1.20 | 0.9595 | 1.01 | 0.81–1.24 | 0.6831 | 0.92 | 0.63–1.35 |
| ||||||||||||
MMP3 | ||||||||||||
rs639752 | G | 0.48 | 0.46 | 0.3896 | 1.09 | 0.90–1.31 | 0.9479 | 0.99 | 0.81–1.21 | 0.0102 | 1.58 | 1.11–2.25 |
rs650108 | G | 0.32 | 0.33 | 0.7042 | 0.96 | 0.79–1.17 | 0.7256 | 1.04 | 0.84–1.28 | 0.0448 | 0.67 | 0.45–0.99 |
rs520540 | A | 0.45 | 0.46 | 0.6774 | 0.96 | 0.80–1.16 | 0.2865 | 0.90 | 0.74–1.10 | 0.0924 | 1.35 | 0.95–1.91 |
rs679620 | A | 0.45 | 0.44 | 0.7039 | 1.04 | 0.86–1.25 | 0.7826 | 0.97 | 0.79–1.19 | 0.0519 | 1.41 | 1.00–2.00 |
rs522616 | G | 0.28 | 0.39 | 0.000003 | 0.62 | 0.51–0.76 | 0.0003 | 0.68 | 0.55–0.84 | 0.0022 | 0.55 | 0.37–0.81 |
rs3025058 | 5A | 0.41 | 0.41 | 0.9395 | 0.99 | 0.82–1.20 | 0.5099 | 0.93 | 0.76–1.14 | 0.0821 | 1.36 | 0.96–1.93 |
MMP7 | ||||||||||||
rs11568818 | G | 0.42 | 0.42 | 0.7878 | 1.03 | 0.85–1.24 | 0.6497 | 1.05 | 0.86–1.28 | 0.7246 | 0.94 | 0.66–1.34 |
| ||||||||||||
MMP9 | ||||||||||||
rs3918253 | C | 0.51 | 0.47 | 0.1493 | 1.15 | 0.95–1.38 | 0.0266 | 0.80 | 0.66–0.97 | 0.2550 | 0.82 | 0.57–1.16 |
rs17576 | G | 0.31 | 0.32 | 0.7042 | 0.96 | 0.78–1.17 | 0.8695 | 0.98 | 0.79–1.22 | 0.6280 | 0.91 | 0.62–1.33 |
rs17577 | G | 0.11 | 0.12 | 0.8298 | 0.97 | 0.72–1.29 | 0.6063 | 0.92 | 0.68–1.26 | 0.8139 | 1.07 | 0.63–1.80 |
| ||||||||||||
MMP10 | ||||||||||||
rs17293607 | T | 0.15 | 0.18 | 0.0602 | 0.78 | 0.60–1.01 | 0.0711 | 0.78 | 0.59–1.02 | 0.6971 | 0.91 | 0.57–1.45 |
| ||||||||||||
MMP13 | ||||||||||||
rs478927 | G | 0.37 | 0.34 | 0.1400 | 1.19 | 0.94–1.48 | 0.0905 | 1.23 | 0.97–1.57 | 0.3157 | 0.78 | 0.49–1.26 |
rs2252070 | G | 0.34 | 0.33 | 0.7859 | 1.03 | 0.84–1.25 | 0.6330 | 1.05 | 0.85–1.29 | 0.1854 | 0.77 | 0.53–1.13 |
| ||||||||||||
MMP14 | ||||||||||||
rs1042704 | A | 0.14 | 0.13 | 0.7171 | 1.05 | 0.80–1.38 | 0.9188 | 0.98 | 0.73–1.32 | 0.0551 | 1.55 | 0.99–2.44 |
| ||||||||||||
MMP16 | ||||||||||||
rs7828497 | G | 0.32 | 0.26 | 0.0125 | 1.30 | 1.05–1.60 | 0.0182 | 1.30 | 1.05–1.61 | 0.3107 | 1.22 | 0.83–1.78 |
rs2616490 | G | 0.39 | 0.37 | 0.3350 | 1.10 | 0.90–1.32 | 0.1529 | 1.16 | 0.95–1.42 | 0.2491 | 0.81 | 0.56–1.16 |
| ||||||||||||
MMP25 | ||||||||||||
rs2360167 | T | 0.24 | 0.22 | 0.6027 | 1.06 | 0.85–1.32 | 0.7500 | 1.04 | 0.82–1.32 | 0.4212 | 1.18 | 0.79–1.77 |
| ||||||||||||
MMP27 | ||||||||||||
rs2509010 | T | 0.23 | 0.23 | 0.9885 | 1.00 | 0.80–1.25 | 0.9578 | 1.01 | 0.80–1.27 | 0.7531 | 1.07 | 0.71–1.61 |
rs11225389 | A | 0.17 | 0.19 | 0.1915 | 0.85 | 0.67–1.08 | 0.0977 | 0.80 | 0.62–1.04 | 0.1533 | 1.35 | 0.89–2.03 |
| ||||||||||||
TIMP1 | ||||||||||||
rs5906435 | T | 0.28 | 0.25 | 0.2301 | 1.16 | 0.91–1.48 | 0.7173 | 1.05 | 0.81–1.36 | 0.0446 | 1.54 | 1.01–2.36 |
rs6520279 | C | 0.43 | 0.42 | 0.5119 | 1.16 | 0.91–1.48 | 0.8497 | 1.02 | 0.81–1.29 | 0.4273 | 1.17 | 0.79–1.74 |
| ||||||||||||
TIMP2 | ||||||||||||
rs8179096 | T | 0.08 | 0.13 | 0.0004 | 0.57 | 0.41–0.77 | 0.0018 | 0.59 | 0.42–0.82 | 0.0007 | 0.23 | 0.09–0.58 |
rs9894526 | T | 0.47 | 0.45 | 0.3055 | 1.10 | 0.91–1.33 | 0.2676 | 1.12 | 0.92–1.36 | 0.9223 | 0.98 | 0.69–1.40 |
P≤ 0.002 indicates statistical significance under Bonferroni correction (in bold).
The following SNPs were non informative or presented minor allele frequency < 10% in the studied population and therefore excluded from the association analyses: rs28730814 (MMP2), rs3025065 and rs11606831 (MMP3), rs11568818 (MMP7), rs17860973 and rs17860971 (MMP10), rs12295719 (MMP13), rs17123036 (MMP14), rs61995943 and rs12099177 (MMP27), rs9747145 (TIMP2), rs34586282 and rs34334473 (TIMP3), and rs3755724 (TIMP4). TIMP2 rs4789940 showed deviation from Hardy-Weinberg equilibrium and was also excluded from further analyses.