From: A new efficient method to detect genetic interactions for lung cancer GWAS
Gene(s) 1 | SNP 1 (GRCh37/hg19) | Gene Region 1 | Alleles (Major/Minor) | MAFa (1000 Genomes) | Gene(s) 2 | SNP 2 (GRCh37/hg19) | Gene Region 2 | Alleles (Major/Minor) | MAF (1000 Genomes) | ES-MDR Test Score | OncoArray-genotyped (HRa) | Log-rank test statistic | Permutation P value |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
BRCA1 | rs749410065 | delTa | –/T | NAa | CBR1, LOC100133286 | rs151043730 | missense, ncRNAa | G/A | 0.001 | 13.77 | 1.24 | 65.74 | < 0.0001 |
BRCA1 | rs749410065 | delTa | –/T | NAa | NAPG | rs3865365 | near 5′ end of genes | G/A | 0.06 | 13.43 | 1.23 | 61.74 | < 0.0001 |
C6orf10 | rs16870005 | Intron | C/T | 0.01 | BRCA1 | rs749410065 | delTa | –/T | NAa | 13.42 | 1.25 | 67.66 | < 0.0001 |
C1orf21, LOC107985236 | rs7535067 | Intron, 3′ UTRa | C/A,T | 0.19 | BRCA1 | rs749410065 | delTa | –/T | NAa | 13.39 | 1.24 | 61.92 | < 0.0001 |
PSMB9, LOC100294145 | rs57092860 | Intergenic | T/C,G | 0.01 | BRCA1 | rs749410065 | delTa | –/T | NAa | 13.37 | 1.25 | 67.82 | < 0.0001 |
CTNND2 | rs7732411 | Intron | T/C | 0.08 | BRCA1 | rs749410065 | delTa | –/T | NAa | 13.32 | 1.25 | 67.53 | < 0.0001 |
TRAM2-AS1, LOC730101 | rs182398206 | Intergenic | A/G | 0.01 | BRCA1 | rs749410065 | delTa | –/T | NAa | 13.30 | 1.25 | 70.95 | < 0.0001 |
MIR4417, MIR4689 | rs6698924 | Intergenic | A/C | 0.02 | BRCA1 | rs749410065 | delTa | –/T | NAa | 13.29 | 1.25 | 68.74 | < 0.0001 |
BRCA1 | rs749410065 | delTa | –/T | NAa | TFAP2C, BMP7 | rs186132350 | Intergenic | T/A | 0.01 | 13.29 | 1.25 | 69.79 | < 0.0001 |
HRAT92, PRKAR1B | rs142263110 | Intergenic | G/A | 0.002 | BRCA1 | rs749410065 | delTa | –/T | NAa | 13.28 | 1.25 | 69.36 | < 0.0001 |