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Table 3 Logistic regression tests: Top 20 SNPs among 95 genotyped/imputed JAK2 SNPs in V617F -positive MPNs

From: Genetic association between germline JAK2polymorphisms and myeloproliferative neoplasms in Hong Kong Chinese population: a case–control study

  Alleles b Minor Allele Freq.   Allelic Test d
SNP a 1 2 Cases Controls OR (95% CI) c P asym P emp
rs12342421 (S8)e C G 0.6172 0.3011 3.55 (2.59-4.87) 3.76 × 10−15 2.00 × 10−5
rs12347727 G A 0.5508 0.2734 3.33 (2.43-4.56) 7.72 × 10−14 2.00 × 10−5
rs2225125 G A 0.5508 0.2755 3.30 (2.41-4.53) 1.18 × 10−13 2.00 × 10−5
rs1327494 G A 0.5508 0.2755 3.30 (2.41-4.53) 1.18 × 10−13 2.00 × 10−5
rs11794778 T G 0.5508 0.2798 3.26 (2.38-4.47) 2.38 × 10−13 2.00 × 10−5
rs12340895 (S13)e G C 0.5664 0.3000 3.27 (2.37-4.51) 4.68 × 10−13 2.00 × 10−5
rs10974914 A G 0.5547 0.3032 3.18 (2.30-4.40) 2.46 × 10−12 2.00 × 10−5
rs10974916 A G 0.5547 0.3043 3.17 (2.29-4.38) 2.94 × 10−12 2.00 × 10−5
rs2183137 G A 0.5508 0.2989 3.11 (2.26-4.28) 3.02 × 10−12 2.00 × 10−5
rs7851556 T C 0.5547 0.3064 3.14 (2.27-4.34) 4.79 × 10−12 2.00 × 10−5
rs7043489 C A 0.5547 0.3064 3.14 (2.27-4.34) 4.79 × 10−12 2.00 × 10−5
rs11794708 A G 0.4258 0.1702 2.67 (2.02-3.53) 5.21 × 10−12 2.00 × 10−5
rs10974921 A T 0.4258 0.1702 2.67 (2.02-3.53) 5.21 × 10−12 2.00 × 10−5
rs7030260 A C 0.5547 0.3202 3.05 (2.20-4.23) 2.00 × 10−11 2.00 × 10−5
rs10974922 T C 0.5547 0.3213 3.04 (2.20-4.22) 2.25 × 10−11 2.00 × 10−5
rs12349785 C G 0.5195 0.2830 2.95 (2.14-4.06) 3.35 × 10−11 2.00 × 10−5
rs966871 T A 0.5391 0.3021 2.86 (2.09-3.92) 5.80 × 10−11 2.00 × 10−5
rs3824433 T C 0.5312 0.3000 2.88 (2.09-3.95) 7.73 × 10−11 2.00 × 10−5
rs1159782 C T 0.5195 0.2936 2.89 (2.09-3.99) 1.16 × 10−10 2.00 × 10−5
rs10974944 (S9)e G C 0.5234 0.2957 2.87 (2.08-3.96) 1.50 × 10−10 2.00 × 10−5
  1. Abbreviations: SNP, single nucleotide polymorphism; OR, odds ratio; P asym , asymptotic P value; P emp , empirical P value.
  2. aThe SNPs are listed in ascending order in terms of their P asym among the top 20 most significantly associated JAK2 SNPs in V617F-positive MPN patients. Association was tested by logistic regression with adjustment for sex and age.
  3. bAlleles 1 and 2 represent the minor and major alleles of that SNP respectively. There are 128 cases and 470 controls.
  4. cCalculated for minor allele (allele 1) with major allele (allele 2) as the reference allele.
  5. dAllele frequencies were calculated by logistic regression with sex and age as covariates to give the P asym value. Multiple comparisons were corrected by 50,000 permutations to give the P emp value.
  6. eThese three SNPs (S8, S9 and S13) were directly genotyped in this study while the rest were imputed by Beagle v3.2 [41].