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Table 4 Top-one-way models identified by ES-MDR 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) Log-rank Test score OncoArray-genotyped (HRa) Permutation P value
LINC00708, LOC105755953 10 rs12358150 8735744 Intergenic C/T 0.26 340.90 20.51 < 0.0001
GTF2IP1, PMS2P5 7 rs149743903 74711828 Intergenic T/C NAa 295.80 6.39 < 0.0001
PPP2R2B, STK32A 5 rs76601208 146581977 Intron C/T 0.002 180.30 22.83 < 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
UTP23, RAD21 8 rs10105870 117807762 Intergenic G/A 0.15 113.00 27.64 < 0.0001
VPS8 3 rs112047443 184701960 Intron A/T NAa 93.30 19.57 < 0.0001
BRCA1 17 rs749410065 41196821 delTa -/T NAa 62.20 1.24 < 0.0001
ATR 3 rs529613417 142285472 Intron A/T 0.001 57.00 5.48 < 0.0001
B3GNT2, TMEM17 2 rs11526118 62647317 Intron G/A 0.16 46.00 23.01 0.0033
  1. aChr, chromosome; bp, base pair; MA, minor allele frequency; detT, NC_000017.10:g.41196821delT; NA, not available; HR, hazard ratio