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Table 2 Exhaustive haplotype analyses for variable-sized sliding windows across 19 genotyped JAK2 SNPs for V617F -positive MPNs a

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

   SW with Omnibus Test P emp  < .05 Most Significant Omnibus Test
SNPs, No. SWs, No. SWs, No. First SW Last SW SW P asym P emp
1 19 14 b S1 S18 S8 d 3.76 × 10−15 2.00 × 10−5
2 18 17 c S1…S2 S18…S19 S8…S9 2.13 × 10−14 2.00 × 10−5
3 17 17 S1…S3 S17…S19 S8…S10 6.33 × 10−14 2.00 × 10−5
4 16 16 S1…S4 S16…S19 S7…S10 8.25 × 10−13 2.00 × 10−5
5 15 15 S1…S5 S15…S19 S8…S12 4.45 × 10−12 2.00 × 10−5
6 14 14 S1…S6 S14…S19 S8…S13 2.75 × 10−12 2.00 × 10−5
7 13 13 S1…S7 S13…S19 S8…S14 2.21 × 10−12 2.00 × 10−5
8 12 12 S1…S8 S12…S19 S8…S15 9.00 × 10−12 2.00 × 10−5
9 11 11 S1…S9 S11…S19 S6…S14 2.38 × 10−11 2.00 × 10−5
10 10 10 S1…S10 S10…S19 S6…S15 9.09 × 10−12 2.00 × 10−5
11 9 9 S1…S11 S9…S19 S6…S16 3.03 × 10−11 2.00 × 10−5
12 8 8 S1…S12 S8…S19 S6…S17 6.69 × 10−11 2.00 × 10−5
13 7 7 S1…S13 S7…S19 S6…S18 1.21 × 10−10 2.00 × 10−5
14 6 6 S1…S14 S6…S19 S6…S19 2.60 × 10−10 2.00 × 10−5
15 5 5 S1…S15 S5…S19 S4…S18 3.02 × 10−9 2.00 × 10−5
16 4 4 S1…S16 S4…S19 S4…S19 1.97 × 10−9 2.00 × 10−5
17 3 3 S1…S17 S3…S19 S3…S19 2.74 × 10−9 2.00 × 10−5
18 2 2 S1…S18 S2…S19 S2…S19 2.96 × 10−8 2.00 × 10−5
19 1 1 S1…S19 S1…S19 S1…S19 6.72 × 10−8 2.00 × 10−5
  1. Abbreviations: SNP, single nucleotide polymorphism; SW, sliding window; P asym , asymptotic P value; P emp , empirical P value.
  2. aThe SW is shown as Sx…Sy, where Sx is the first SNP and Sy is the last SNP of the SW for JAK2 gene. Please refer to Table 1 for the identity of the SNP concerned. Each sliding window was tested by an omnibus test adjusted for sex and age (implemented in PLINK). Multiple comparisons were corrected by running 50,000 permutations to give the P emp value. The smallest P emp value generated after permutation is the same for all fixed-size SWs (2 × 10−5); note that the lowest P emp value achievable with 50,000 permutations is 2 × 10−5. The most significant results for each fixed-size SW are shown in the three rightmost columns. Note that, among all the 190 SWs tested, S8 always appears in the most significant SW.
  3. bOf the nineteen SNPs tested, five (S5, S6, S11, S16, and S19) did not give P emp  < 0.05.
  4. c All the SWs gives P emp  < 0.05 except S5…S6.
  5. dOf all the 190 SWs tested, S8 (i.e. rs12342421) alone gives the most significant result for association with V617F-positive MPNs.