Fig. 4: Facial effect of face-associated SNPs with a focus on the nose. | Nature Communications

Fig. 4: Facial effect of face-associated SNPs with a focus on the nose.

From: Combined genome-wide association study of facial traits in Europeans increases explained variance and improves prediction

Fig. 4: Facial effect of face-associated SNPs with a focus on the nose.

a Illustration of the total effects of 253 lead SNPs on the face, based on regional-PVE across 8 facial regions. The 3D template facial image in a is adapted from White et al.82 published under an Open Access license (CC BY 4.0), see http://creativecommons.org/licenses/by/4.0/. b Enlarged frontal and lateral views of the nose with 14 landmark points highlighted in c and d, and Supplementary Note 6. The scale indicates the p-value of deviation of the landmark from the average in c and d, which is derived from the association test between PRS and landmark coordinates using linear regression. PRS analysis and its effects on the nose are illustrated for: c for L21–L24 and L23–L26, and d for L7–L8 and L8–L9. Each figure is divided into three sections: PRS effects on the nose (left, enlarged nasal view), population profiling (middle, violin plots), and gene contributions (right). In the nasal views, landmarks significantly associated with standardized PRS are marked with orange dots (3 times positive effect offset) or blue dots (3 times negative effect offset). Connecting lines visually represent nasal variation, with scaled distances shown in the top left. Nasal images reconstructed at mean PRS ± 3 SD are framed in orange (+3SD) and blue (−3SD) and generated using a 3D graph auto-encoder (see the “Methods” section). The overall effect of increasing PRS is described in text at the top left. The violin plots show standardized PRS results for four major populations from the 1000 Genomes Project (African, AFR, N = 504; European, EUR, N = 504; East Asian, EAS, N = 503; South Asian, SAS, N = 489), with the band indicating the median, the box representing the first and third quartiles, and whiskers extending 1.5 times the interquartile range. Gene contribution plots on the right list the top regions accounting for 50% of PRS variance. The 3D template facial image in b–d was generated from the average covariate-adjusted facial shape of all RS participants (N = 4242).

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