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Table 1 Allelic association tests for 19 genotyped tag SNPs of the JAK2 gene in V617F -positive MPNs

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

  Alleles b Genotype counts (11/12/22) Minor allele (1) freq.   Allelic test d
SNP rs a 1 2 Cases Controls Cases Controls OR (95% CI) c P asym P emp
rs3808850 (S1) T A 10/53/65 66/230/174 0.2852 0.3851 0.61 (0.45-0.84) 0.0022 0.0213
rs7849191 (S2) T C 8/40/80 26/233/170 0.2188 0.3904 0.43 (0.30-0.60) 6.35 × 10−7 4.00 × 10−5
rs7046736 (S3) A C 40/69/19 65/225/180 0.5820 0.3777 2.53 (1.85-3.46) 5.92 × 10−9 2.00 × 10−5
rs2149555 (S4) T C 20/85/23 41/194/235 0.4883 0.2936 2.51 (1.82-3.48) 2.01 × 10−8 2.00 × 10−5
rs1536798 (S5) A C 28/57/43 59/228/183 0.4414 0.3681 1.30 (0.97-1.74) 0.0765 0.4500
rs10815148 (S6) A T 9/59/60 20/167/283 0.3008 0.2202 1.60 (1.15-2.23) 0.0057 0.0509
rs2149556 (S7) C T 8/63/57 86/245/139 0.3086 0.4436 0.51 (0.37-0.71) 5.23 × 10−5 0.0005
rs12342421 (S8) C G 52/54/22 43/197/230 0.6172 0.3011 3.55 (2.59-4.87) 3.76 × 10−15 2.00 × 10−5
rs10974944 (S9) G C 29/76/23 40/198/232 0.5234 0.2957 2.87 (2.08-3.96) 1.50 × 10−10 2.00 × 10−5
rs10119004 (S10) G A 10/71/47 121/248/101 0.3555 0.5213 0.46 (0.33-0.63) 1.65 × 10−6 4.00 × 10−5
rs10974947 (S11) A G 1/31/96 15/129/326 0.1289 0.1691 0.73 (0.48-1.11) 0.1414 0.6676
rs12343867 (S12) C T 22/80/23 39/186/245 0.4844 0.2809 2.60 (1.89-3.58) 3.80 × 10−9 2.00 × 10−5
rs12340895 (S13) G C 40/65/23 41/200/229 0.5664 0.3000 3.27 (2.37-4.51) 4.68 × 10−13 2.00 × 10−5
rs12343065 (S14) T C 28/77/23 41/201/228 0.5195 0.3011 2.80 (2.03-3.87) 3.80 × 10−10 2.00 × 10−5
rs7857730 (S15) G T 10/61/57 89/245/136 0.3164 0.4500 0.53 (0.38-0.73) 0.0001 0.0012
rs3824432 (S16) A G 1/37/90 26/148/296 0.1523 0.2128 0.67 (0.45-0.98) 0.0382 0.2711
rs7847294 (S17) A C 2/55/71 63/240/167 0.2305 0.3894 0.39 (0.27-0.56) 3.74 × 10−7 2.00 × 10−5
rs3780378 (S18) C T 8/58/62 84/239/147 0.2891 0.4330 0.49 (0.36-0.68) 2.25 × 10−5 0.0002
rs10815162 (S19) C G 2/43/83 40/182/248 0.1836 0.2787 0.59 (0.41-0.84) 0.0037 0.0336
  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 sequential order from the 5’ end to the 3’ end of the sense strand of the JAK2 gene. They are also designated S1 to S19 for the sake of easy reference and discussion. Fifteen SNPs (all except S5, S6, S11 and S16) are associated with V617F-positive MPNs. Of these 15 MPN-associated SNPs, 7 have been reported previously (S1, S2, S3, S8, S9, S12 and S13) and 8 are novel and have not been reported previously (S4, S7, S10, S14, S15, S17, S18 and S19).
  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 compared by logistic regression with adjustment for sex and age to give the P asym value. Multiple comparisons were corrected by 50,000 permutations to give the P emp value.