Table 1. The top 10 and MHC interaction regions associated with NPC susceptibility.
| Region A | Region B | Interaction p-value | Suggestive Interaction Numberd | ||||||||||||
| Chr. | SNPa | Location | Distance (bp)b | NearestGene | Single- locus P c | Chr. | SNPa | Location | Distance (bp)b | Nearest Gene | Single- locus P c | Stage 1 | Stage 2 | Combined | |
| 7p15 | rs2237353 | intron | CREB5 | 5.03E-01 | 17q22 | rs1607979 | upstream | 566,730 | KIF2B | 3.78E-01 | 9.96E-08*** | 5.87E-04** | 9.86E-11*** | 2 | |
| 7q11 | rs6460664 | intron | WBSCR17 | 2.18E-01 | 9q33 | rs2300932 | intron | C5 | 6.11E-01 | 9.63E-09*** | 9.76E-03* | 8.86E-10*** | 3 | ||
| 4q26 | rs6821696 | downstream | 5,428 | MIR1973 | 2.49E-01 | 10q26 | rs1380439 | intron | ADAM12 | 6.89E-01 | 2.12E-07*** | 8.37E-04** | 8.90E-10*** | 1 | |
| 2q36 | rs10933155 | upstream | 13,764 | RHBDD1 | 5.33E-01 | 21q22 | rs1888469 | intron | ERG | 9.91E-01 | 3.67E-08*** | 1.45E-03* | 1.04E-09*** | 1 | |
| 7p21 | rs10487781 | intron | DGKB | 4.38E-01 | 7q31 | rs17154507 | upstream† | 54,319 | DLD | 8.30E-01 | 4.58E-08*** | 2.35E-03* | 1.43E-09*** | 1 | |
| 9p21 | rs1332173 | upstream | 175,899 | TUSC1 | 8.01E-01 | 16p13 | rs2127065 | intron | RBFOX1 | 3.49E-01 | 3.64E-07*** | 4.24E-04** | 1.76E-09*** | 6 | |
| 2p23 | rs6726261 | upstream† | 11,931 | ADCY3 | 4.51E-01 | 9q21 | rs11140659 | upstream | 120,855 | NTRK2 | 4.23E-01 | 2.21E-07*** | 3.85E-03* | 1.92E-09*** | 1 |
| 2p16 | rs7589636 | upstream | 444,753 | VRK2 | 5.47E-01 | 2p16 | rs730402 | upstream | 513,286 | MIR4432 | 2.73E-02 | 4.59E-07*** | 1.47E-03* | 2.11E-09*** | 5 |
| 1p34 | rs4660176 | intron | KCNQ4 | 3.08E-01 | 7q36 | rs740576 | intron | DPP6 | 8.98E-01 | 6.33E-08*** | 2.97E-03* | 2.11E-09*** | 1 | ||
| 5p15 | rs4571472 | intron | FBXL7 | 3.10E-01 | 10q21 | rs7075349 | intron† | ZNF365 | 2.74E-01 | 6.28E-07*** | 1.93E-03* | 3.38E-09*** | 1 | ||
| MHC | |||||||||||||||
| 6p21 | rs2523849 | intron | HCG22 | 4.48E-01 | 6p21 | rs4947296 | downstream | 20,822 | C6orf15 | 1.90E-01 | 4.28E-07*** | 1.97E-03* | 8.42E-09*** | 3 | |
| 6p21 | rs7761965 | downstream | 48,764 | HLA-B | 8.90E-01 | 6p21 | rs2596501 | downstream | 1,298 | HLA-B | 4.68E-02 | 2.64E-07*** | 7.40E-03* | 1.81E-08*** | 2 |
a The most significant SNP pairs within the region.
b Distance between the most significant SNP and its nearest gene.
c Single-locus association p-value from the discovery data set.
d The number of significant interactions within this region. For detailed information, see Table S3.
SNP located within the putative transcription regulatory region annotated by the UCSC genome browser (http://genome.ucsc.edu/).
Permuted p-value<0.01 after 10 000 permutations.
Permuted p-value<0.001 after 10 000 permutations.
Permuted p-value<0.0001 after 10 000 permutations. For detailed permutation p-values, see Table S3.