Table 3. Markers achieving genome-wide significance in GWAS of 3,379 NSCLP cases and 8,593 controls of Chinese Han and prioritized genes in each significant SNP.
| Loci | SNP | BP | Allele | PMeta | OR | Phet* | Notable gene(s) |
|---|---|---|---|---|---|---|---|
| Novel loci: | |||||||
| 2p25.1 | rs287980 | 9971366 | G/A | 1.94E−08 | 0.83 | 0.8120 | TAF1B |
| 2p25.1 | rs287982 | 9972442 | G/A | 6.15E−09 | 0.82 | 0.8981 | TAF1B |
| 4p16.2 | rs34246903 | 4794195 | C/A | 4.45E−08 | 0.85 | 0.2344 | MSX1 |
| 4p16.2 | rs1907989 | 4818925 | A/G | 1.58E−08 | 0.85 | 0.1130 | MSX1 |
| 4q28.1 | rs908822 | 124906257 | A/G | 4.33E−08 | 1.31 | 0.0545 | SPRY1 |
| 5p12 | rs10462065 | 44068846 | A/C | 1.12E−08 | 1.22 | 0.4835 | FGF10 |
| 6p24.3 | rs9381107 | 9469238 | A/G | 2.72E−09 | 0.83 | 0.0900 | OFCC1/TFAP2A |
| 8p11.23 | rs13317 | 38269514 | G/A | 3.96E−08 | 0.85 | 0.4601 | FGFR1 |
| 8q22.1 | rs12681366 | 95401265 | G/A | 2.35E−10 | 0.83 | 0.5965 | RAD54B |
| 8q22.1 | rs957448 | 95541302 | G/A | 9.60E−13 | 0.81 | 0.1260 | RAD54B |
| 9q22.32 | rs10512248 | 98259703 | C/A | 5.10E−10 | 0.82 | 0.2026 | PTCH1 |
| 12q13.13 | rs3741442 | 53346750 | G/A | 3.72E−12 | 1.22 | 0.9598 | KRT18 |
| 12q13.2 | rs705704 | 56435412 | A/G | 1.29E−09 | 1.22 | 0.9839 | RPS26 |
| 12q21.1 | rs2304269 | 72080272 | G/A | 1.32E−12 | 0.81 | 0.3903 | TMEM19 |
| 12q21.1 | rs7967428 | 72089040 | G/A | 3.08E−12 | 0.81 | 0.3871 | TMEM19 |
| 14q22.1 | rs7148069 | 51839645 | A/G | 1.69E−08 | 1.22 | 0.2538 | LINC00640 |
| 14q32.13 | rs1243572 | 95379499 | G/A | 3.52E−10 | 1.20 | 0.1138 | GSC/DICER1 |
| 14q32.13 | rs1243573 | 95379583 | C/A | 8.61E−10 | 1.20 | 0.1178 | GSC/DICER1 |
| 17q21.32 | rs4968247 | 44988703 | A/G | 8.70E−10 | 0.83 | 0.8605 | WNT9B |
| 17q21.32 | rs1838105 | 45008935 | A/G | 1.31E−11 | 1.22 | 0.3543 | WNT9B |
| Reported loci: | |||||||
| 1p22.1 | rs481931 | 94570016 | A/C | 1.06E−12 | 0.80 | 0.3687 | ARHGAP29 |
| 1p22.1 | rs4147803 | 94582293 | G/C | 7.97E−12 | 0.81 | 0.8369 | ARHGAP29 |
| 1q32.2 | rs861020 | 209977111 | A/G | 1.30E−14 | 1.31 | 0.5428 | IRF6 |
| 1q32.2 | rs642961 | 209989270 | A/G | 2.76E−15 | 1.32 | 0.6061 | IRF6 |
| 1q32.2 | rs2064163 | 210048819 | A/C | 8.60E−19 | 0.77 | 0.9625 | IRF6 |
| 1q32.2 | rs9430019 | 210050794 | A/G | 1.68E−12 | 1.25 | 0.6420 | IRF6 |
| 2p24.2 | rs10172734 | 16733054 | G/A | 2.89E−20 | 0.74 | 0.4992 | FAM49A |
| 2p24.2 | rs7552 | 16733928 | A/G | 5.83E−22 | 0.73 | 0.5814 | FAM49A |
| 8q21.3 | rs12543318 | 88868340 | A/C | 8.80E−12 | 0.81 | 0.2050 | MMP16 |
| 8q21.3 | rs1034832 | 88918331 | C/A | 1.35E−10 | 0.82 | 0.2243 | MMP16 |
| 8q24.21 | rs7845615 | 129888794 | A/G | 1.03E−10 | 1.27 | 0.8110 | MYC |
| 8q24.21 | rs7017252 | 129950844 | A/G | 8.47E−16 | 1.60 | 0.8960 | MYC |
| 9q22.2 | rs7871395 | 92209587 | A/G | 6.06E−09 | 1.21 | 0.5782 | GADD45G |
| 10q25.3 | rs6585429 | 118893231 | G/A | 7.14E−13 | 0.81 | 0.9967 | VAX1 |
| 13q31.1 | rs9545308 | 80639405 | A/C | 2.00E−09 | 1.29 | 0.8103 | SPRY2 |
| 16p13.3 | rs2283487 | 3969886 | G/A | 1.27E−10 | 0.83 | 0.9121 | CREBBP |
| 16p13.3 | rs17136624 | 3996282 | A/G | 3.82E−10 | 1.24 | 0.5269 | CREBBP |
| 17p13.1 | rs2872615 | 8914693 | G/A | 8.81E−12 | 0.82 | 0.5224 | NTN1 |
| 17p13.1 | rs1880646 | 8929845 | A/G | 1.69E−11 | 1.22 | 0.4104 | NTN1 |
| 17q22 | rs227731 | 54773238 | C/A | 8.83E−09 | 1.19 | 0.5623 | NOG |
| 20q12 | rs6129653 | 39275603 | A/G | 8.57E−12 | 1.23 | 0.5970 | MAFB |
GWAS, genome-wide association study; NSCLP, non-syndromic cleft lip with palate; OR, odds ratio; SNP, single-nucleotide polymorphism.
Genome-wide significance is defined as P<5 × 10−8; SNP positions are reported according to Build 37 and their alleles are coded based on the positive strand; alleles (minor/major); meta-analysis is of NSCLP GWAS and NSCLP replication using fixed model; the P-value using Cochran–Mantel–Haenszel test; OR is calculated based on minor allele.
*Phet: P-value for heterozygosity test using logistic regression test and Bonferroni correction and Phet>0.05 was considered to signify no heterogeneity.