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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
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BMC Genomics

ISSN: 1471-2164

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