Table 1. SNPs significantly associated (p<5×10−8) with facial shape phenotypes from European discovery GWAS meta-analysis (RS, TwinksUK, ALSPAC, and PITT), and their multi-ethnic replication (UYG, CANDELA and QIMR).
| Discovery meta-analysis | Replication | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| (N = 10,115) | (N = 7,917) | ||||||||
| Region | SNP | Nearest Gene | EA | OA | Trait | Beta | P | Q | Com. P |
| Novel face-associated loci | |||||||||
| 1p36.22 | rs143353512 | CASZ1 | A | G | Prn-AlL | −0.29 | 6.44 × 10−9 | 0.73 | 0.0001 |
| 1p36.13 | rs200243292 | ARHGEF19 | I | T | EnR-ChL | −0.11 | 1.46 × 10−8 | 0.54 | 0.0640 |
| 1p31.2 | rs77142479 | RPE65 | C | A | EnL-Sn | −0.08 | 7.65 × 10−9 | 0.90 | 0.0121 |
| 2p12 | rs10202675 | LRRTM4 | T | C | EnR-AlR | −0.26 | 4.43 × 10−8 | 0.40 | 0.0226 |
| 2q31.1 | rs2884836 | KIAA1715 | T | C | ExR-ChR | −0.09 | 3.04 × 10−8 | 0.52 | 0.1096 |
| 3q12.1 | rs113663609 | CMSS1 | A | G | EnR-ChR | −0.12 | 3.46 × 10−8 | 0.96 | 0.0782 |
| 4q28.1 | rs12504954 | INTU | A | G | Prn-AlL | −0.09 | 3.03 × 10−10 | 0.52 | 0.0015 |
| 6p22.3 | rs2225718 | RNF144B | C | T | EnR-AlR | −0.09 | 2.97 × 10−8 | 0.60 | 0.0071 |
| 6p21.2 | rs7738892 | KIF6 | T | C | EnR-N | 0.11 | 1.34 × 10−8 | 0.09 | 0.0018 |
| 8p23.2 | rs1700048 | CSMD1 | C | A | ExR-ChL | −0.22 | 3.94 × 10−8 | 0.73 | 0.1131 |
| 8q21.3 | rs9642796 | DCAF4L2 | A | G | AlL-Ls | −0.11 | 4.52 × 10−8 | 0.07 | 0.3090 |
| 10q22.1 | rs201719697 | SUPV3L1 | A | D | ExL-AlL | −0.28 | 3.42 × 10−8 | 0.66 | NA |
| 12q24.21 | rs1863716 | TBX3 | A | C | Prn-AlR | −0.09 | 1.47 × 10−10 | 0.53 | 2.45 × 10−5 |
| 13q14.3 | rs7325564 | LINC00371 | T | C | N-Prn | 0.09 | 1.34 × 10−8 | 0.16 | 0.3519 |
| 14q32.2 | rs1989285 | C14orf64 | G | C | N-Prn | −0.10 | 4.54 × 10−8 | 0.82 | 0.0019 |
| 16q12.1 | rs16949899 | SALL1 | T | G | ExR-ChL | −0.13 | 3.35 × 10−8 | 0.76 | 0.8912 |
| 16q12.2 | rs7404301 | RPGRIP1L | G | A | AlL-Ls | −0.09 | 3.49 × 10−9 | 0.43 | 2.87 × 10−7 |
| Previously reported face-associated loci | |||||||||
| 1p12 | rs1229119 | TBX15 | T | C | ExR-ChR | 0.08 | 2.25 × 10−8 | 0.26 | 0.1219 |
| 2q36.1 | rs34032897 | PAX3 | G | A | EnR-N | 0.14 | 1.96 × 10−17 | 0.04 | 0.0020 |
| 4q31.3 | rs6535972 | SFRP2 | C | G | EnL-AlL | 0.12 | 3.51 × 10−12 | 0.12 | 5.89 × 10−12 |
| 9q22.31 | rs2230578 | ROR2 | C | T | EnL-Sn | 0.09 | 9.02 × 10−9 | 0.66 | 1.09 × 10−6 |
| 17q24.3 | rs8077906 | CASC17 | A | G | Prn-EnL | −0.09 | 3.00 × 10−11 | 0.24 | 0.0505 |
| 17q24.3 | rs35473710 | SOX9 | G | A | AlR-ChL | 0.19 | 3.95 × 10−8 | 0.37 | 0.2634 |
| 20p11.22 | rs4813454 | PAX1 | T | C | AlL-AlR | −0.10 | 2.32 × 10−11 | 0.58 | 0.0002 |
Except rs2230578 (3'-UTR of ROR2) and rs7738892 (a synonymous variant of KIF6), all SNPs are intronic or intergenic. Gene symbols in bold indicate successful replication after Bonferroni correction of 24 loci (p<2.1×10−3). Meta P in bold indicates study-wide significance in the discovery analysis after multiple trait correction (p<1.2×10−9). Replication P in bold means significant after Bonferroni correction for multiple tests (p<2.1×10−3). Q: p-value from the Cochran's Q test for testing heterogeneity between discovery cohorts. EA and OA, the effect allele and the another allele. Com. P: p-values from a combined test of dependent tests. NA, not available.