Supplementary Material
Genetic determination of human facial morphology: links
between cleft-lips and normal variation
Boehringer S1,2,*, van der Lijn F3,6, Liu F3, Günther M4, Sinigerova S2, Nowak S5,
Ludwig KU6, Herberz R6, Klein S7, Hofman A8, Uitterlinden A.G9, Niessen WJ7,10,
Breteler MMB8, van der Lugt A11, Wurtz RP4, Nöthen MM5,6, Horsthemke B2,
Wieczorek D2, Mangold E5†, Kayser M3†
†
these authors contributed equally
1
Medical Statistics and Bioninformatics, Leiden University Medical Center, Leiden, The
Netherlands
2
Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
3
Department of Forensic Molecular Biology, Erasmus MC University Medical Center
Rotterdam, Rotterdam, The Netherlands
4
Institut für Neuroinformatik, Ruhr-Universität Bochum, Bochum, Germany
5
Institute of Human Genetics, University of Bonn, Bonn, Germany
6
Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
7
Departments of Medical Informatics and Radiology, Erasmus MC University Medical
Center Rotterdam, Rotterdam, The Netherlands
8
Department of Epidemiology, Erasmus MC University Medical Center Rotterdam,
Rotterdam, The Netherlands
9
Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam,
Rotterdam, The Netherlands
10
Faculty of Applied Sciences, Delft University of Technology, The Netherlands
11
Department of Radiology, Erasmus MC University Medical Center Rotterdam,
Rotterdam, The Netherlands
The following document provides supplementary information to the above publication.
Table S1 contains descriptive information of the markers used in the study. Table S2
describes association results under the genotype model. Tables S3 and S4 list sexstratified analyses according to the additive and genotype model, respectively. Table S5
contains coefficients of the prediction models and table S6 describes significance levels
of covariates used in the analysis.
Table S1
Genotype frequencies, HWE goodness-of-fit tests and data missing rates for the SNPs in
the study. Column Major lists the major allele for each locus. Gt1, Gt2, Gt3 are
genotype frequencies for homozygotes (major allele), heterozygotes and homozygotes
(minor allele), respectively.
Locus
1p21
17q22
8q24
8q24
15q13
1q32
20q12
17q22
13q31
2p21
10q25
Marker
rs560426
rs17760296
rs16903544
rs987525
rs1258763
rs642961
rs13041247
rs227731
rs9574565
rs7590268
rs7078160
Essen
Rotterdam
Major HWE Gt1
Gt2
Gt3
Miss HWE Gt1
Gt2
Gt3
Miss
C
0.740 0.296 0.492 0.212 0.0%
T
0.957 0.663 0.303 0.034 0.2% 0.776 0.702 0.271 0.028 0.0%
T
0.783 0.792 0.195 0.014 2.1% 0.371 0.801 0.186 0.013 0.0%
C
0.197 0.632 0.314 0.054 1.9% 0.711 0.581 0.365 0.054 0.0%
A
0.731 0.481 0.430 0.089 0.6% 0.822 0.473 0.428 0.099 0.0%
G
0.618 0.616 0.333 0.051 0.2% 0.419 0.617 0.333 0.051 0.0%
T
0.732 0.355 0.478 0.167 0.0%
A
0.363 0.330 0.506 0.165 0.2% 0.879 0.293 0.495 0.213 0.0%
C
0.438 0.583 0.369 0.048 1.7% 0.727 0.588 0.355 0.056 0.0%
T
0.590 0.568 0.366 0.067 0.8% 0.627 0.622 0.331 0.047 0.0%
G
0.205 0.672 0.305 0.023 0.2% 0.057 0.709 0.258 0.033 0.0%
Table S2
Association tests for width measurements of the face (Phenotype) with a genotype
model. Column RA denotes the reference allele, column beta 1 and beta 2 denote the
effects of the heterozygous and homozygous variant genotype, respectively. p denotes
the corresponding P-value for a two degree of freedom test. Standard deviations are
given in parentheses. Variances were standardized to 1. Comb lists combined P-values.
Phenotype Locus Marker
Nose
1p21 rs560426
17q22 rs17760296
8q24 rs16903544
8q24 rs987525
15q13 rs1258763
1q32 rs642961
20q12 rs13041247
17q22 rs227731
13q31 rs9574565
2p21 rs7590268
10q25 rs7078160
Bicygoma- 1p21 rs560426
tic distance 17q22 rs17760296
8q24 rs16903544
8q24 rs987525
15q13 rs1258763
1q32 rs642961
20q12 rs13041247
17q22 rs227731
13q31 rs9574565
2p21 rs7590268
10q25 rs7078160
RA
C
T
T
C
A
G
T
A
C
T
G
C
T
T
C
A
G
T
A
C
T
G
beta 1
0.08 (0.10)
-0.13 (0.12)
-0.06 (0.10)
-0.33 (0.09)
0.03 (0.10)
0.02 (0.10)
-0.09 (0.09)
0.11 (0.09)
0.04 (0.10)
-0.16 (0.09)
-0.13 (0.11)
-0.08 (0.10)
0.01 (0.09)
-0.14 (0.09)
-0.14 (0.10)
0.00 (0.09)
-0.00 (0.09)
-0.04 (0.09)
Essen
beta 2
p
0.45 (0.20) 0.0779
1.13 (0.41) 0.0109
-0.22 (0.16) 0.3796
-0.37 (0.18) 0.0004
0.06 (0.22) 0.9309
0.25 (0.13) 0.1116
0.19 (0.23) 0.3470
0.12 (0.15) 0.4206
0.02 (0.34) 0.8976
-0.16 (0.21) 0.2087
0.62 (0.48) 0.1931
-0.04 (0.22) 0.7208
-0.08 (0.15) 0.8295
-0.06 (0.19) 0.3008
-0.05 (0.13) 0.3379
-0.55 (0.20) 0.0163
0.18 (0.20) 0.6515
-0.09 (0.34) 0.8852
Beta 1
-0.29 (0.16)
-0.04 (0.16)
0.20 (0.18)
0.01 (0.15)
-0.12 (0.15)
0.09 (0.15)
-0.39 (0.15)
0.29 (0.16)
-0.06 (0.15)
-0.05 (0.15)
0.11 (0.16)
-0.06 (0.20)
0.36 (0.20)
0.16 (0.23)
-0.28 (0.18)
0.04 (0.18)
0.19 (0.19)
-0.24 (0.19)
0.12 (0.20)
0.13 (0.18)
-0.38 (0.18)
0.34 (0.20)
Rotterdam
Beta 2
p
-0.06 (0.20) 0.159
-0.50 (0.42) 0.500
-0.93 (0.60) 0.142
0.12 (0.31) 0.930
-0.28 (0.24) 0.450
-0.80 (0.32) 0.025
-0.05 (0.20) 0.025
0.04 (0.20) 0.145
-0.08 (0.30) 0.896
-0.05 (0.33) 0.944
-0.18 (0.40) 0.684
0.19 (0.25) 0.513
0.48 (0.52) 0.136
0.08 (0.72) 0.770
-0.81 (0.38) 0.051
-0.50 (0.30) 0.194
-0.78 (0.40) 0.058
-0.15 (0.26) 0.440
-0.04 (0.25) 0.731
0.16 (0.39) 0.755
-0.47 (0.43) 0.093
0.15 (0.49) 0.228
Comb
p
0.8207
0.9889
0.5872
0.0023
0.6027
0.1534
0.5082
0.5325
0.7142
0.9577
0.4859
0.2560
0.5611
0.6343
0.7567
0.6585
0.7023
0.8341
Table S3
Sex-startified association tests for width measurements of the face (Phenotype) with an
additive model. Column RA denotes the reference allele, column beta the effect of the
variant allele with p the corresponding P-value. Standard deviations are given in
parentheses. Variances were standardized to 1. Comb lists combined P-values.
Essen
Rotterdam Comb
Phenotype Locus
SNP RA beta
p
beta
p
p
Females
Nose widtth 1p21
17q22
8q24
8q24
15q13
1q32
20q12
17q22
13q31
2p21
10q25
Bicygomatic 1p21
distance
17q22
8q24
8q24
15q13
1q32
20q12
17q22
13q31
2p21
10q25
Males
Nose
1p21
17q22
8q24
8q24
15q13
1q32
20q12
17q22
13q31
2p21
10q25
Bicygomatic 1p21
distance
17q22
8q24
8q24
15q13
1q32
20q12
17q22
13q31
2p21
10q25
rs560426 C
rs17760296 T
rs16903544 T
rs987525 C
rs1258763 A
rs642961 G
rs13041247 T
rs227731 A
rs9574565 C
rs7590268 T
rs7078160 G
rs560426 C
rs17760296 T
rs16903544 T
rs987525 C
rs1258763 A
rs642961 G
rs13041247 T
rs227731 A
rs9574565 C
rs7590268 T
rs7078160 G
0.18 (0.10)
0.22 (0.16)
-0.12 (0.08)
-0.20 (0.09)
-0.02 (0.09)
0.17 (0.07)
-0.06 (0.09)
0.10 (0.08)
0.04 (0.10)
-0.15 (0.09)
0.09 (0.14)
0.04 (0.09)
-0.03 (0.08)
-0.03 (0.08)
-0.00 (0.08)
-0.04 (0.08)
0.05 (0.09)
0.04 (0.10)
0.0667
0.1622
0.1285
0.0269
0.8383
0.0180
0.4905
0.1826
0.7260
0.0985
0.5298
0.6268
0.7156
0.7170
0.9625
0.6427
0.5673
0.6757
0.02 (0.12)
0.08 (0.17)
-0.15 (0.20)
0.21 (0.15)
-0.05 (0.14)
-0.19 (0.15)
-0.06 (0.13)
-0.01 (0.12)
-0.25 (0.15)
-0.07 (0.15)
0.07 (0.17)
0.10 (0.16)
0.00 (0.22)
0.04 (0.27)
-0.44 (0.20)
-0.33 (0.18)
-0.11 (0.20)
-0.15 (0.17)
-0.05 (0.16)
-0.14 (0.20)
-0.60 (0.20)
0.14 (0.22)
0.8917
0.6591
0.4732
0.1568
0.7035
0.2228
0.6188
0.9238
0.0939
0.6586
0.6771
0.5595
0.9880
0.8941
0.0235
0.0630
0.5671
0.3759
0.7632
0.4622
0.0028
0.5245
0.0617
0.7750
0.8875
0.0427
0.4496
0.1985
0.1953
0.3621
0.5940
0.1954
0.6163
0.5297
0.3448
0.5796
0.7947
0.5508
0.4399
0.5181
rs560426 C
rs17760296 T
rs16903544 T
rs987525 C
rs1258763 A
rs642961 G
rs13041247 T
rs227731 A
rs9574565 C
rs7590268 T
rs7078160 G
rs560426 C
rs17760296 T
rs16903544 T
rs987525 C
rs1258763 A
rs642961 G
rs13041247 T
rs227731 A
rs9574565 C
rs7590268 T
rs7078160 G
0.05 (0.13)
-0.30 (0.16)
-0.00 (0.13)
-0.34 (0.12)
0.13 (0.14)
-0.03 (0.13)
0.10 (0.16)
0.06 (0.12)
0.04 (0.15)
-0.08 (0.15)
-0.21 (0.18)
-0.27 (0.13)
0.00 (0.13)
-0.20 (0.14)
-0.10 (0.12)
-0.25 (0.14)
0.04 (0.13)
-0.16 (0.15)
0.6980
0.0672
0.9929
0.0031
0.3739
0.8048
0.5111
0.6231
0.7994
0.5773
0.2378
0.0406
0.9994
0.1597
0.3997
0.0840
0.7459
0.3040
-0.13 (0.16)
-0.32 (0.21)
0.23 (0.24)
-0.17 (0.18)
-0.22 (0.16)
-0.08 (0.18)
-0.12 (0.15)
0.10 (0.15)
0.18 (0.18)
-0.00 (0.19)
-0.00 (0.20)
0.07 (0.19)
0.66 (0.24)
0.23 (0.29)
-0.24 (0.21)
0.07 (0.20)
-0.04 (0.22)
-0.07 (0.19)
0.05 (0.19)
0.38 (0.22)
0.01 (0.23)
0.36 (0.24)
0.4098
0.1208
0.3366
0.3318
0.1760
0.6484
0.4444
0.5154
0.3341
0.9879
0.9860
0.6899
0.0064
0.4331
0.2627
0.7193
0.8456
0.7052
0.8113
0.0777
0.9583
0.1457
0.5733
0.8263
0.5877
0.0014
0.6917
0.8048
0.2606
0.7201
0.8351
0.4779
0.8195
0.0208
0.8413
0.1947
0.5726
0.8855
0.7753
0.7983
Table S4
Sex-stratified association tests for width measurements of the face (Pheno) with a
genotype model. Column RA denotes the reference allele, column beta 1 and beta 2
denote the effects of the heterozygous and homozygous variant genotype, respectively. p
denotes the corresponding P-value for a two degree of freedom test. Standard deviations
are given in parentheses. Variances were standardized to 1. Comb lists combined Pvalues.
Pheno Locus Marker
Females
1p21 rs560426
Nose
width
17q22 rs17760296
8q24 rs16903544
8q24 rs987525
15q13 rs1258763
1q32 rs642961
20q12 rs13041247
17q22 rs227731
13q31 rs9574565
2p21 rs7590268
10q25 rs7078160
Bicygo- 1p21 rs560426
17q22 rs17760296
matic
distance 8q24 rs16903544
8q24 rs987525
15q13 rs1258763
1q32 rs642961
20q12 rs13041247
17q22 rs227731
13q31 rs9574565
2p21 rs7590268
10q25 rs7078160
Males
1p21 rs560426
Nose
width
17q22 rs17760296
8q24 rs16903544
8q24 rs987525
15q13 rs1258763
1q32 rs642961
20q12 rs13041247
17q22 rs227731
13q31 rs9574565
2p21 rs7590268
10q25 rs7078160
1p21 rs560426
Bicygomat
17q22 rs17760296
ic distance
8q24 rs16903544
8q24 rs987525
15q13 rs1258763
1q32 rs642961
20q12 rs13041247
17q22 rs227731
13q31 rs9574565
2p21 rs7590268
10q25 rs7078160
beta 1
Essen
beta 2
p
Beta 1
Rotterdam
Beta 2
p
Comb
p
C
T
T
C
A
G
T
A
C
T
G
C
T
T
C
A
G
T
A
C
T
G
0.14 (0.12)
0.03 (0.15)
-0.11 (0.11)
-0.31 (0.10)
0.09 (0.12)
0.11 (0.12)
-0.07 (0.10)
0.11 (0.11)
0.08 (0.11)
-0.13 (0.10)
-0.02 (0.12)
-0.02 (0.11)
0.02 (0.10)
-0.05 (0.10)
-0.12 (0.11)
0.08 (0.10)
0.05 (0.11)
-0.02 (0.11)
0.49 (0.28)
1.51 (0.43)
-0.27 (0.19)
-0.23 (0.22)
-0.29 (0.22)
0.36 (0.14)
-0.10 (0.24)
0.19 (0.16)
-0.18 (0.50)
-0.34 (0.27)
0.76 (0.67)
0.22 (0.25)
-0.12 (0.18)
-0.02 (0.21)
0.04 (0.15)
-0.38 (0.20)
0.10 (0.24)
0.46 (0.36)
0.136
0.002
0.273
0.011
0.262
0.040
0.776
0.387
0.709
0.249
0.519
0.637
0.732
0.910
0.379
0.081
0.849
0.433
-0.10 (0.20)
0.13 (0.20)
0.04 (0.23)
0.29 (0.19)
-0.04 (0.19)
0.01 (0.19)
-0.30 (0.20)
0.52 (0.21)
-0.32 (0.19)
0.00 (0.19)
0.08 (0.20)
0.14 (0.27)
0.03 (0.26)
0.15 (0.31)
-0.39 (0.25)
-0.04 (0.24)
-0.21 (0.25)
-0.10 (0.25)
0.16 (0.27)
-0.09 (0.25)
-0.54 (0.25)
0.23 (0.27)
0.06 (0.25)
-0.08 (0.56)
-1.41 (0.78)
0.21 (0.41)
-0.12 (0.31)
-0.90 (0.43)
-0.01 (0.27)
-0.08 (0.25)
-0.33 (0.39)
-0.27 (0.39)
0.10 (0.54)
0.18 (0.33)
-0.08 (0.71)
-0.54 (0.98)
-1.02 (0.53)
-1.02 (0.41)
0.01 (0.55)
-0.33 (0.36)
-0.14 (0.33)
-0.42 (0.53)
-1.33 (0.56)
-0.01 (0.66)
0.768
0.795
0.183
0.280
0.927
0.101
0.244
0.006
0.199
0.773
0.912
0.826
0.989
0.751
0.072
0.041
0.703
0.657
0.595
0.710
0.011
0.692
0.1141
0.9940
0.6854
0.1262
0.1935
0.2946
0.3656
0.5895
0.6819
0.3831
0.8752
0.6766
0.5373
0.7678
0.7289
0.0955
0.5948
0.5320
C
T
T
C
A
G
T
A
C
T
G
C
T
T
C
A
G
T
A
C
T
G
-0.06 (0.17)
-0.40 (0.19)
0.05 (0.17)
-0.37 (0.16)
-0.09 (0.17)
-0.15 (0.18)
-0.13 (0.16)
0.12 (0.17)
-0.02 (0.20)
-0.20 (0.20)
-0.22 (0.17)
0.01 (0.18)
-0.33 (0.18)
-0.17 (0.18)
-0.10 (0.16)
-0.11 (0.17)
-0.04 (0.17)
0.39 (0.29)
0.20 (0.09)
-0.11 (0.32)
-0.64 (0.26)
0.76 (0.41)
0.01 (0.27)
0.82 (0.45)
0.02 (0.29)
0.38 (0.18)
0.15 (0.30)
-0.66 (0.36)
-0.01 (0.27)
-0.10 (0.35)
-0.17 (0.25)
-0.88 (0.42)
0.33 (0.31)
-0.90 (0.41)
0.325
0.000
0.888
0.013
0.124
0.641
0.109
0.762
0.077
0.482
0.112
0.998
0.184
0.619
0.109
0.408
0.088
-0.50 (0.26)
-0.24 (0.24)
0.38 (0.28)
-0.34 (0.23)
-0.21 (0.23)
0.18 (0.24)
-0.49 (0.24)
0.01 (0.25)
0.24 (0.23)
-0.12 (0.23)
0.14 (0.25)
-0.30 (0.31)
0.73 (0.29)
0.18 (0.34)
-0.17 (0.28)
0.14 (0.28)
0.66 (0.28)
-0.41 (0.29)
0.07 (0.30)
0.38 (0.28)
-0.19 (0.28)
0.48 (0.30)
-0.20 (0.31)
-0.95 (0.65)
-0.41 (0.93)
-0.00 (0.47)
-0.46 (0.37)
-0.70 (0.48)
-0.08 (0.32)
0.22 (0.31)
0.20 (0.48)
0.38 (0.58)
-0.40 (0.58)
0.19 (0.37)
1.06 (0.76)
0.74 (1.06)
-0.60 (0.54)
0.06 (0.45)
-1.53 (0.57)
0.04 (0.39)
0.08 (0.38)
0.77 (0.57)
0.66 (0.67)
0.33 (0.74)
0.131
0.249
0.343
0.328
0.399
0.207
0.105
0.733
0.563
0.676
0.643
0.293
0.022
0.699
0.497
0.874
0.001
0.279
0.966
0.211
0.436
0.274
0.6790
0.1119
0.8140
0.0013
0.9968
0.7216
0.2718
0.9172
0.8397
0.5744
0.0375
0.9433
0.5573
0.7351
0.9311
0.2570
0.6203
RA
Table S5
Coefficients for the predictive models of the Rotterdam (R) and Essen (E) studies. For
the additive model, a single coefficient is given whereas for the genotype model the first
coefficient is for the heterozygous genotype and the second coefficient is given for the
minor homozygous genotype. The phenotypes (nose width, Nose; bicygomatic distance,
BD) were standardized to zero mean and standard deviation one.
Nose, genotype, E
Nose, additive, E BD additive, R
0.000
0.000
0.000
0.116
0.005
0.315
0.063
rs17760296
0.000
0.000
0.037
0.000
rs16903544
0.000
0.000
-0.310
-0.002
rs987525
0.000
-0.139
-0.091
-0.170
rs1258763
-0.004
0.000
-0.020
0.000
rs642961
0.000
-0.063
rs13041247
0.000
0.008
0.067
rs227731
0.096
0.000
0.115
0.000
rs9574565
0.000
0.041
-0.266
0.033
rs7590268
0.000
0.000
0.232
0.000
rs7078160
0.000
Marker
(Intercept)
rs560426
Table S6
Descriptive measures for the significance levels for covariates age and sex across all
unstratified tests performed for tables 1 and S2. Min., 1st Qu., Median, Mean, 3rd Qu.
Max. are the minimum, 1st quartile, median, mean, 3rd quartile and maximum,
respectively, of the P-values of coefficients not being zero.
Sex
Essen
Min.
1st Qu.
Median
Mean
3rd Qu.
Max.
Min.
1st Qu.
Median
Mean
3rd Qu.
Max.
0.035
0.049
0.209
0.230
0.399
0.460
Rotterdam
5.4E-021
7.1E-021
1.2E-003
1.4E-003
2.7E-003
3.2E-003
Age
0.003
0.009
0.048
0.054
0.096
0.122
0.0E+000
0.0E+000
6.1E-255
8.4E-253
9.9E-253
1.0E-251