Skip to main content

Table 1 The top 11 loci for Gemcitabine (A) and the top 27 loci for AraC (B) that were associated with drug response-IC50 values

From: Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines

 Top SNP rsID  Lowest R  Lowest P  Nearby gene  Chr  Position  MAF Region Number of SNPs in each locus
(A) Gemcitabine
rs10513968 −0.382 1.04E-06 DOK6 18 65434121 0.445 Intron 9
rs7719624 −0.370 4.22E-06 TGFBI 5 135405465 0.448 Intron 28
rs2274870 0.362 4.33E-06 NIPSNAP3A 9 106555035 0.371 Coding 7
rs316838 −0.345 1.21E-05 PLD5* 1 240387283 0.093 Intron 12
rs2638094 −0.339 1.72E-05 ZNF215* 11 6938064 0.679 Flanking_3UTR 5
rs2290344 0.339 1.75E-05 PIGB 15 53407088 0.253 Coding 9
rs3129890 0.332 2.67E-05 HLA-DRA* 6 32522251 0.340 Flanking_3UTR 23
rs2928445 −0.331 2.76E-05 IPMK 10 58816782 0.267 Flanking_3UTR 23
rs4392391 −0.318 5.78E-05 C3orf23 3 44247970 0.419 Downstream 15
rs12522395 0.318 6.58E-05 MASS1* 5 90246274 0.215 Intron 4
rs13171512 −0.313 7.857E-05 PIK3R1 5 68000787 0.462 Flanking_3UTR 4
(B) AraC
rs10495285 0.393 4.13E-07 KIAA0133 (URB2) 1 227871618 0.171 Downstream 2
rs1450679 0.389 5.20E-07 SMC2L1 9 106066633 0.098 Flanking_3UTR 8
rs6128386 0.375 1.38E-06 LOC149773 20 56626955 0.466 Upstream 4
rs2172820 −0.373 1.63E-06 TUSC3 8 15370039 0.256 Flanking_5UTR 13
rs2857891 −0.372 1.75E-06 ZNF215* 11 6919533 0.101 Intron 6
rs9512755 −0.361 3.67E-06 LNX2 13 27056229 0.055 Flanking_5UTR 4
rs888468 −0.356 5.08E-06 FGF6 12 4403640 0.184 Flanking_3UTR 5
rs2653165 −0.347 9.28E-06 PLD5* 1 240432905 0.207 Intron 7
rs11215416 −0.346 9.57E-06 IGSF4 11 114582537 0.147 Intron 7
rs10060641 0.335 1.90E-05 MASS1* 5 90249006 0.216 Intron 7
rs5989586 0.336 1.94E-05 HDHD1A 23 6757306 0.457 Flanking_3UTR 8
rs216465 −0.330 2.76E-05 GOSR1 17 25880801 0.494 Flanking_3UTR 12
rs856548 −0.326 3.29E-05 TNS3 7 46730993 0.296 Flanking_3UTR 8
rs6689258 0.325 3.40E-05 GPR137B 1 234362702 0.267 Flanking_5UTR 2
rs3794794 −0.325 3.61E-05 CPD 17 25744867 0.477 Intron 10
rs7192 0.322 4.10E-05 HLA-DRA* 6 32519624 0.371 Coding 11
rs4572738 0.322 4.45E-05 CAST1 3 55799452 0.321 Intron 8
rs1433446 0.319 5.05E-05 TMEM83 15 85351874 0.109 Flanking_5UTR 5
rs300962 0.320 5.47E-05 LOC51334 5 119909842 0.269 Intron 15
rs6441911 0.315 6.20E-05 RIS1 3 45322523 0.055 Flanking_5UTR 6
rs1159388 0.314 6.61E-05 DCAMKL1 13 35544706 0.172 Intron 11
rs718979 0.313 6.82E-05 UBE3A 15 23325370 0.394 Flanking_5UTR 6
rs1955412 0.309 8.74E-05 FLRT2 14 85082547 0.21 Intron 11
  1. Each locus contained at least 2 SNPs within 50 kb with P values <10-4. R values represent correlation coefficients for the association. Number of SNPs indicates the number of significantly associated SNPs in the locus. rsID indicates the most significant SNP associated with drug cytotoxicity in the locus. * = common to both gemcitabine and AraC.