Neighboring-Nucleotide Effects on Single Nucleotide Polymorphisms: A Study of 2.6 Million Polymorphisms Across the Human Genome

Table 1.

Proportion of Neighboring Nucleotides

Position (bp) 5′ side 3′ side Both sides
A (%) C (%) G (%) T (%) A (%) C (%) G (%) T (%) A (%) C (%) G (%) T (%)
 1 30.98 25.35 18.76 24.92 25.11 18.85 25.51 30.53 28.04 22.10 22.13 27.72
 2 28.51 23.05 20.29 28.15 28.33 20.24 22.97 28.46 28.42 21.65 21.63 28.30
 3 29.39 21.14 19.99 29.48 29.62 20.03 21.04 29.30 29.51 20.58 20.52 29.39
 4 29.94 21.22 20.39 28.45 28.64 20.39 21.20 29.77 29.29 20.81 20.79 29.11
 5 29.64 20.91 20.71 28.75 28.92 20.70 20.80 29.57 29.28 20.80 20.76 29.16
 6 29.33 20.53 21.44 28.70 28.87 21.40 20.56 29.17 29.10 20.96 21.00 28.94
 7 29.66 20.14 20.92 29.28 29.38 20.98 20.16 29.48 29.52 20.56 20.54 29.38
 8 29.77 20.43 21.07 28.73 28.97 21.03 20.41 29.59 29.37 20.73 20.74 29.16
 9 29.16 20.82 20.79 29.23 29.36 20.81 20.79 29.04 29.26 20.82 20.79 29.14
10 29.06 20.73 20.95 29.26 29.41 20.94 20.69 28.95 29.24 20.84 20.82 29.11
11–20 29.36 20.70 20.84 29.10 29.31 20.83 20.66 29.20 29.34 20.77 20.75 29.15
21–50 29.20 20.92 20.82 29.06 29.25 20.83 20.88 29.05 29.21 20.89 20.86 29.04
51–100 29.32 20.69 20.73 29.26 29.39 20.78 20.66 29.17 29.32 20.76 20.72 29.19
101–200 29.41 20.65 20.65 29.30 29.41 20.71 20.64 29.24 29.32 20.76 20.73 29.18
201–300 29.61 20.37 20.38 29.63 29.68 20.52 20.44 29.36 29.48 20.63 20.60 29.29
Genome 29.55 20.44 20.46 29.54 29.55 20.44 20.46 29.54 29.55 20.44 20.46 29.54

  • ↵Position relative to the polymorphic site. For positions farther than 10 bp, the average proportion of each nucleotide in the range is shown.

  • ↵The average proportion of four nucleotides in the human genome based on NCBI Human RefSeq.

This Article

  1. Genome Res. 12: 1679-1686

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