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Table 3 Association results of SNPs within the SOX9 locus (5643 discovery GWAS participants and 1940 SOX9 replication participants)

From: Identification of five novel genetic loci related to facial morphology by genome-wide association studies

SNP CHR:Position (bp)a Distance from 5′ of SOX9 Coded allele (AF) Non-coded allele Nose Traits Association results   Meta-analysis (Phase 1 + SOX9 replication)
  beta ± se P-value   beta ± se P-value Q I2
rs9915190 7:66,654,223 974 kb A(0.45) C Nasal tip protrusion Phase 1 −0.015 ± 0.003 6.03 × 10−6   − 0.016 ± 0.003 1.72 × 10 − 9 0.72 0.00
  Phase 1 (3 SNPs conditional) −0.016 ± 0.003 2.08 × 10− 6      
  SOX9 replication set − 0.017 ± 0.004 7.04 × 10− 5      
Nasal bridge depth Phase 1 − 0.198 ± 0.063 1.68 × 10−3   − 0.112 ± 0.052 3.05 × 10− 2 0.02 82.56
  Phase 1 (3 SNPs conditional) −0.204 ± 0.063 1.22 × 10− 3      
  SOX9 replication set 0.066 ± 0.091 4.65 × 10−1      
Profile nasal area Phase 1 − 0.017 ± 0.003 3.10 × 10− 7   − 0.016 ± 0.003 2.34 × 10 − 9 0.61 0.00
  Phase 1 (3 SNPs conditional) − 0.017 ± 0.003 1.26 × 10− 7      
  SOX9 replication set −0.014 ± 0.005 1.91 × 10− 3      
Nasolabial angle Phase 1 0.007 ± 0.002 3.21 × 10− 3   0.009 ± 0.002 2.68 × 10− 5 0.34 0.00
  Phase 1 (3 SNPs conditional) 0.008 ± 0.002 1.69 × 10− 3      
  SOX9 replication set 0.011 ± 0.004 1.73 × 10− 3      
Profile nasal angle Phase 1 0.005 ± 0.001 5.79 × 10− 6   0.004 ± 0.001 4.07 × 10− 7 0.47 0.00
  Phase 1 (3 SNPs conditional) 0.005 ± 0.001 1.02 × 10− 6      
  SOX9 replication set 0.003 ± 0.001 1.83 × 10− 2      
rs1859979 7:66,940,738 688 kb C(0.46) T Nasal tip protrusion Phase 1 0.018 ± 0.003 1.56 × 10− 7   0.017 ± 0.003 1.91 × 10 − 10 0.68 0.00
  Phase 1 (3 SNPs conditional) 0.017 ± 0.003 7.50 × 10− 7      
  SOX9 replication set 0.016 ± 0.004 2.98 × 10− 4      
Nasal bridge depth Phase 1 0.331 ± 0.064 2.21 × 10− 7   0.272 ± 0.052 1.92 × 10− 7 0.11 61.76
  Phase 1 (3 SNPs conditional) 0.323 ± 0.064 4.76 × 10− 7      
  SOX9 replication set 0.152 ± 0.091 9.33 × 10− 2      
Profile nasal area Phase 1 0.022 ± 0.003 8.07 × 10 − 11   0.018 ± 0.003 7.22 × 10 − 12 0.09 64.77
  Phase 1 (3 SNPs conditional) 0.020 ± 0.003 1.39 × 10 − 9      
  SOX9 replication set 0.012 ± 0.005 6.59 × 10− 3      
Nasolabial angle Phase 1 −0.011 ± 0.002 9.86 × 10− 6   − 0.013 ± 0.002 1.13 × 10 − 10 0.11 60.21
  Phase 1 (3 SNPs conditional) − 0.011 ± 0.002 2.10 × 10− 5      
  SOX9 replication set −0.018 ± 0.004 8.09 × 10− 7      
Profile nasal angle Phase 1 − 0.006 ± 0.001 2.37 × 10 − 9   − 0.007 ± 0.001 9.58 × 10 − 15 0.63 0.00
  Phase 1 (3 SNPs conditional) − 0.006 ± 0.001 2.53 × 10 − 9      
  SOX9 replication set − 0.007 ± 0.001 8.17 × 10− 7      
rs9910003 7:67,390,279 238 kb A(0.28) G Nasal tip protrusion Phase 1 0.015 ± 0.004 4.05 × 10− 5      
  Phase 1 (3 SNPs conditional) 0.007 ± 0.004 9.07 × 10− 2      
  SOX9 replication set        
Nasal bridge depth Phase 1 0.038 ± 0.071 5.90 × 10− 1      
  Phase 1 (3 SNPs conditional) − 0.077 ± 0.079 3.33 × 10− 1      
  SOX9 replication set        
Profile nasal area Phase 1 0.007 ± 0.004 7.71 × 10− 2      
  Phase 1 (3 SNPs conditional) 0.001 ± 0.004 8.50 × 10− 1      
  SOX9 replication set        
Nasolabial angle Phase 1 −0.011 ± 0.003 1.12 × 10− 4      
  Phase 1 (3 SNPs conditional) −0.004 ± 0.003 1.99 × 10− 1      
  SOX9 replication set        
Profile nasal angle Phase 1 −0.004 ± 0.001 3.87 × 10− 4      
  Phase 1 (3 SNPs conditional) 0.000 ± 0.001 8.06 × 10− 1      
  SOX9 replication set        
rs2193054 17:67,537,404 91 kb C(0.47) G Nasal tip protrusion Phase 1 0.019 ± 0.003 1.93 × 10 − 8   0.017 ± 0.003 1.85 × 10 − 10 0.35 0.00
  Phase 1 (3 SNPs conditional) 0.015 ± 0.004 3.26 × 10− 5      
  SOX9 replication set 0.013 ± 0.004 1.74 × 10− 3      
Nasal bridge depth Phase 1 0.165 ± 0.062 8.02 × 10−3   0.130 ± 0.051 1.10 × 10− 2 0.33 0.00
  Phase 1 (3 SNPs conditional) 0.211 ± 0.070 2.50 × 10− 3      
  SOX9 replication set 0.057 ± 0.091 5.30 × 10− 1      
Profile nasal area Phase 1 0.010 ± 0.003 1.33 × 10− 3   0.010 ± 0.003 8.14 × 10− 5 0.98 0.00
  Phase 1 (3 SNPs conditional) 0.011 ± 0.004 3.62 × 10− 3      
  SOX9 replication set 0.010 ± 0.005 2.25 × 10−2      
Nasolabial angle Phase 1 −0.014 ± 0.002 1.56 × 10 − 8   − 0.013 ± 0.002 2.25 × 10 − 10 0.49 0.00
  Phase 1 (3 SNPs conditional) −0.012 ± 0.003 7.34 × 10− 6      
  SOX9 replication set − 0.011 ± 0.004 3.35 × 10− 3      
Profile nasal angle Phase 1 − 0.007 ± 0.001 1.43 × 10 − 11   − 0.006 ± 0.001 9.01 × 10 − 14 0.24 27.90
  Phase 1 (3 SNPs conditional) −0.007 ± 0.001 1.50 × 10 − 9      
  SOX9 replication set − 0.005 ± 0.001 8.53 × 10− 4      
  1. Bold and underlined text indicates genome-wide significant P values (5 × 10− 8)
  2. CHR chromosome, AF coded allele frequency, Q P-value for Cochrane’s Q statistic, I2 heterogeneity index
  3. aPositions according to NCBI Build 36