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Table 6 Top SNPs selected by cox lasso regression in OncoArray-TRICL data

From: A new efficient method to detect genetic interactions for lung cancer GWAS

Nearest Gene(s) Chra SNP (GRCh37/hg19) Position (bpa) (GRCh37/hg19) Gene region Alleles (Major/Minor) MAFa (1000 Genomes) Test score OncoArray-genotyped (HRa) Permutation P value
BRCA1 17 rs749410065 41196821 delTa –/T NAa 62.20 1.24 < 0.0001
GTF2IP1, PMS2P5 7 rs149743903 35528378 Intergenic C/G NAa 295.80 6.39 < 0.0001
LOC102467079, TOX3 16 rs117142114 52328666 Intergenic T/C 0.02 31.00 1.29 < 0.0001
HYKK 15 rs9788721 78802869 Intron C/T 0.31 86.30 1.41 < 0.0001
MIR3925, PANDAR 6 rs7753169 36614326 Intergenic A/C 0.36 27.90 1.15 < 0.0001
CHRNA5 15 rs16969968 78882925 missense G/A 0.15 86.80 1.41 < 0.0001
KLF5, LINC00392 13 rs138428539 73736950 Intergenic T/C,G 0.01 145.10 6.46 < 0.0001
TULP1, FKBP5 6 rs6906359 35528378 Intron C/T 0.10 135.90 5.76 < 0.0001
CHRNA5 15 rs951266 78878541 Intron G/A 0.16 88.50 1.41 < 0.0001
FAM114A1 4 rs1873195 38891173 Intron C/T 0.20 8.90 0.87 0.0119
  1. aChr, chromosome; NA, not available; bp, base pair; delTa = NC_000017.10:g.41196821delT; MAF, minor allele frequency; HR, hazard ratio