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Table 1 SNP selection for the survival studies.

From: A Kallikrein 15 (KLK15) single nucleotide polymorphism located close to a novel exon shows evidence of association with poor ovarian cancer survival

SNP no Name Rationale Position ObsHET PredHET HWpval MAF
1 rs2659058 Tagged SNP from HapMap 56017918 0.421 0.443 0.0869 0.331
2 rs3212810 Tagged SNP from HapMap and predicted to fall in miRNA binding site 56020548 0.364 0.369 0.6072 0.244
3 rs3212853 Ploymorphic miRNA target site 56020606 0.044 0.041 0.2863 0.037
4 rs3212852 Exon-Intron boundary 56021941 0.038 0.038 1 0.019
5 rs3745522 Tagged SNP from HapMap 56022744 0.349 0.383 0.0013 0.259
6 rs2659056 Tagged SNP from HapMap 56027755 0.383 0.382 1 0.257
7 rs266851 Tagged SNP from HapMap 56028151 0.297 0.306 0.2742 0.189
8 rs16987576 2 bp 3' of exon B, Imp for splicing 56028165 0.003 0.003 1 0.001
9 rs2659055 Predicted in silico to affect HRE 56029044 0.485 0.5 0.3033 0.49
10 rs2163861 Tagged SNP from HapMap 56029204 0.485 0.5 0.2841 0.489
11 rs266853 Predicted in silico to affect TFBS and HRE 56029520 0.001 0.001 1 0.001
12 rs266854 Predicted in silico to affect HRE 56029630 0.004 0.004 1 0.002
13 rs190552 Predicted in silico to affect TFBS and HRE 56030005 0.333 0.346 0.1823 0.222
14 rs266855 Predicted in silico to affect HRE 56030196 0.396 0.413 0.1259 0.292
15 rs266856 Tagged SNP from HapMap 56030318 0.333 0.349 0.1131 0.225
16 rs2739442 Predicted in silico to affect TFBS and HRE 56030985 0.479 0.493 0.2975 0.442
17 rs2033496 Predicted in silico to affect TFBS and HRE 56031019 0.49 0.493 0.8309 0.442
18 rs12978902 Predicted in silico to affect HRE 56031056 0 0 1 0
19 rs2659053 Predicted in silico to affect TFBS and HRE 56032606 0.449 0.472 0.0722 0.382
20 rs2569746 Predicted in silico to affect TFBS and HRE 56032727 0.462 0.487 0.0638 0.42
21 rs35711205 Novel SNP (reported later in NCBI) 56032818 0.296 0.309 0.1212 0.191
22 rs2569747 Predicted in silico to affect TFBS and HRE 56032875 0.459 0.487 0.0346 0.419
  1. ObsHet: Observed heterozygous alleles; PredHET: Predicted heterozygous alleles; HWpval: Hardy-Weinberg equilibrium p value; MAF: Minor allele frequency; HRE: Hormone Response Element; TFBS: Transcription Factor Binding Site
  2. SNPs in the KLK15 gene derived from the HapMap database and those by in silico prediction methods were genotyped in control individuals, and the minor allele frequency (MAF) and HWE were calculated using Haploview 4.2. SNPs in bold were shortlisted for genotyping and survival analysis on the basis on LD calculations.