Table 2 Gene expression for 13 candidate genes showing significant evidence of linkage in the presence of LD in 58 cleft case‐parent trios.
| Gene (region) | SNP | Allele* | T/N† | p value‡ | Expression§ | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Haplotype | Palate lineage | Lip lineage | ||||||||||
| 1 | 2 | 1 | 2 | 3 | 4 | 5 | Affy | SAGE | Affy | SAGE | |||
| SP100 | rs890674 | G | A | 14/4 | 0.049 | 0.033 | W5PA1 | A | A | A | |||
| (2q37.1) | rs1678203 | G | A | 19/11 | W85PS | ||||||||
| rs1678158 | G | A | 13/8 | ||||||||||
| rs33079 | G | A | 7/4 | ||||||||||
| rs890669 | A | G | 14/12 | ||||||||||
| MLPH | rs880931 | G | A | 11/4 | 0.039 | 0.019 | NA | W5PA1 | NA | A | |||
| (2q37.3) | rs1463795 | C | G | 16/6 | 0.049 | ||||||||
| rs8260 | A | G | 10/5 | ||||||||||
| HDAC4 | rs1466094 | G | A | 14/11 | 0.006 | W4PA1 | W4PA1 | W5FNP | W4FNP | ||||
| (2q37.2) | rs1055333 | G | C | 15/7 | 0.036 | 0.004 | 0.013 | W5PA1 | W5PA1 | W5FNP | |||
| rs2121980 | G | A | 20/10 | 0.049 | 0.012 | 0.001 | 0.009 | 0.014 | W6MAX | ||||
| rs2100171 | A | C | 7/5 | ||||||||||
| rs686606 | G | A | 7/3 | 0.038 | |||||||||
| rs1962113 | A | C | 16/4 | 0.028 | |||||||||
| rs291329 | G | A | 18/10 | ||||||||||
| rs1015458 | A | G | 10/4 | ||||||||||
| rs1403607 | G | A | 9/3 | ||||||||||
| rs1403608 | G | A | 9/3 | ||||||||||
| rs2018414 | G | A | 15/8 | ||||||||||
| rs2176046 | G | A | 6/5 | ||||||||||
| rs925736 | A | G | 14/13 | ||||||||||
| ADH1C | rs1614972 | G | A | 19/9 | 0.002 | 0.002 | 0.002 | 0.004 | A | A | A | A | |
| (4q22) | rs1662058 | A | G | 24/6 | 0.001 | 0.001 | 0.001 | 0.001 | 0.001 | ||||
| rs904096 | A | C | 25/8 | 0.005 | 0.007 | 0.010 | 0.010 | 0.015 | |||||
| rs1789911 | A | G | 24/8 | 0.008 | 0.011 | 0.009 | 0.016 | ||||||
| rs1693482 | G | A | 24/8 | 0.008 | 0.006 | 0.010 | |||||||
| rs1662051 | C | A | 25/8 | 0.005 | 0.007 | ||||||||
| rs980972 | C | A | 24/8 | 0.008 | |||||||||
| LEF1 | rs1291490 | G | A | 8/6 | A | W5PA1 | W4FNP | W5FNP | |||||
| (4q23–25) | rs898518 | A | C | 20/8 | 0.040 | 0.030 | 0.046 | W5FNP | |||||
| rs744369 | G | A | 22/8 | 0.028 | 0.036 | ||||||||
| rs1460405 | G | A | 5/2 | 0.038 | |||||||||
| rs956237 | A | G | 22/8 | 0.033 | 0.033 | ||||||||
| rs922168 | G | A | 13/7 | ||||||||||
| C6orf105 | rs210910 | G | A | 17/7 | 0.050 | 0.035 | 0.028 | W5PA1 | A | A | A | ||
| (6p24.1) | rs210903 | G | A | 20/7 | 0.020 | 0.048 | |||||||
| rs210895 | A | G | 18/12 | ||||||||||
| CD44 | rs353612 | G | A | 13/5 | 0.020 | 0.023 | W4PA1 | W4PA1 | W5FNP | W4FNP | |||
| (11pter‐p13) | rs353636 | C | A | 15/7 | 0.041 | 0.038 | W5PA1 | W5PA1 | W85UL | W5FNP | |||
| rs713330 | A | G | 19/9 | W6MAX | |||||||||
| rs13347 | G | A | 18/9 | W85PS | |||||||||
| ALX4 | rs729287 | G | A | 19/15 | 0.016 | 0.030 | 0.023 | NA | A | NA | A | ||
| (11p11.2) | rs879238 | G | A | 16/14 | |||||||||
| rs1869480 | C | G | 6/2 | ||||||||||
| SCN3B | rs2027767 | G | A | 14/11 | 0.031 | 0.005 | 0.007 | 0.008 | NA | A | A | A | |
| (11q24.1) | rs1274205 | C | G | 12/1 | 0.005 | 0.001 | 0.004 | 0.001 | 0.001 | ||||
| rs1783901 | G | A | 13/5 | 0.046 | 0.009 | 0.004 | 0.004 | 0.004 | |||||
| rs1148107 | A | C | 8/1 | 0.039 | 0.046 | 0.049 | |||||||
| rs1720340 | A | G | 11/6 | ||||||||||
| rs1783902 | C | A | 11/6 | ||||||||||
| rs1720328 | C | G | 11/6 | ||||||||||
| rs1148085 | A | G | 15/12 | ||||||||||
| ZNF202 | rs558021 | T | C | 16/8 | W4PA1 | A | W4FNP | A | |||||
| (11q23.3) | rs481168 | A | C | 2/1 | W5PA1 | W5FNP | |||||||
| rs10904 | A | G | 16/10 | W6MAX | |||||||||
| rs679597 | A | G | 18/7 | 0.048 | W85PS | ||||||||
| CRHR1 | rs171441 | T | C | 10/3 | W4PA1 | NA | W4FNP | NA | |||||
| (17q12–22) | rs242937 | T | C | 17/14 | W5PA1 | W5FNP | |||||||
| rs242936 | T | C | 11/4 | 0.035 | 0.046 | 0.037 | W6MAX | W6MNP | |||||
| rs242950 | A | G | 10/4 | 0.045 | W85PS | W85UL | |||||||
| rs878887 | T | C | 16/7 | 0.046 | 0.024 | 0.025 | 0.024 | ||||||
| IMP5 | rs242943 | A | G | 16/7 | 0.028 | 0.031 | 0.021 | NA | A | NA | A | ||
| (17q21.31) | rs962885 | C | T | 15/11 | 0.021 | 0.019 | 0.022 | 0.032 | |||||
| MAPT | rs916793 | T | C | 16/8 | 0.041 | 0.025 | W5PA1 | A | W85UL | A | |||
| (17q21.1) | rs1864325 | T | C | 16/8 | 0.048 | 0.025 | 0.025 | W85PS | |||||
| rs1467967 | A | G | 19/13 | 0.026 | 0.025 | 0.026 | |||||||
| rs1467970 | T | G | 16/8 | ||||||||||
| rs242556 | T | A | 12/11 | ||||||||||
| rs754512 | T | A | 16/8 | ||||||||||
| rs1052553 | A | G | 16/8 | ||||||||||
| rs9468 | T | C | 16/8 | ||||||||||
*Overtransmitted alleles are in bold type and the major allele is listed first; †transmission/non‐transmission counts from heterozygous parents; ‡significant p values from single SNP TDT and global p values from haplotype TDT with two, three, four, and five SNPs; §the embryonic structures analysed were: W4PA1, 4th week pharyngeal arch 1; W5PA1, 5th week pharyngeal arch 1; W6MAX, 6th week maxilla; W85PS, 8.5th week palatine shelves; W4FNP, 4th week frontonasal prominence; W5FNP, 5th week frontonasal prominence; W6MNP, 6th week median nasal prominence; W85UL, 8.5th week upper lip. A, absent; NA, not available.