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Table 1 Interaction effects on tRNA p9 site methylation

From: Integrated genomic analysis of mitochondrial RNA processing in human cancers

Cancer p9 Site rs number Chr Position Location Gene N MAF MAF range P value
BRCA 7526 rs3781574 11 33885268 intron LMO2 46 0.161 0.128–0.231 4.61E-11
BRCA 7526 rs17690328 11 33885390 intron LMO2 46 0.135 0.016–0.190 1.17E-08
BRCA 7526 rs317391 17 32174605 intron ASIC2 44 0.085 0.014–0.485 2.46E-09
KIRC 1610 rs258701 7 81761122 intron CACNA2D1 61 0.058 0.072–0.167 8.27E-10
KIRC 8303 rs10266772 7 14132727 Intergenic - 61 0.080 0.079–0.254 2.27E-08
KIRC 10413 rs1028014 8 40698232 intron ZMAT4 64 0.174 0.085–0.236 2.88E-08
KIRC 12146 rs17164416 5 99387447 Intergenic - 65 0.051 0.000–0.188 9.95E-09
LIHC 12146 rs41465346 1 219059708 Intergenic - 48 0.052 0.006–0.304 3.73E-08
LIHC 12146 rs16926871 8 62027498 intron CLVS1 47 0.074 0.038–0.270 1.24E-08
LUAD 585 rs13029285 2 205916078 intron PARD3B 49 0.057 0.003–0.076 1.81E-10
LUAD 10413 rs7328699 13 28615701 intron FLT3 46 0.107 0.000–0.124 9.15E-10
LUAD 10413 rs12591927 15 31833911 intron OTUD7A 44 0.077 0.016–0.289 2.44E-08
LUAD 10413 rs17003208 22 43073031 Intergenic - 45 0.074 0.096–0.431 1.13E-08
LUAD 10413 rs17003212 22 43079754 Intergenic - 46 0.063 0.096–0.434 1.18E-11
LUAD 12146 rs4741498 9 15424938 intron SNAPC3 45 0.063 0.005–0.256 3.68E-08
LUAD 12146 rs7026970 9 15445219 intron SNAPC3 45 0.063 0.040–0.355 3.68E-08
LUAD 12146 rs7046713 9 15458921 intron SNAPC3 45 0.063 0.031–0.357 3.68E-08
LUAD 14734 rs341737 8 2782370 Intergenic - 54 0.107 0.081–0.225 9.86E-09
PRAD 10413 rs7631369 3 1028679 Intergenic - 48 0.070 0.015–0.418 3.45E-08
PRAD 10413 rs7301597 12 30175147 Intergenic - 48 0.050 0.000–0.105 3.85E-09
THCA 585 rs17033484 4 156686737 intron GUCY1B3 54 0.089 0.058–0.187 3.78E-08
THCA 4271 rs2145836 20 47421064 intron PREX1 44 0.054 0.000–0.058 4.41E-08
  1. MAF denotes minor allele frequency of the polymorphism in TCGA data for the specific cancer type, and MAF range denotes the range of minor allele frequencies across continents observed in 1000 Genomes phase 3 data [41]