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Table 2 Nucleotide diversity and neutrality tests for the analysed gene regions

From: Balancing selection is common in the extended MHC region but most alleles with opposite risk profile for autoimmune diseases are neutrally evolving

Gene La Pb Sc θWd πe Tajima's D Fu & Li's D* Fu & Li's F*
     value rankf value rankf value rankf p g value rankf p g value rankf p g
ZSCAN23 3.3 CEU 7 4.96 0.44 6.52 0.66 0.87 0.78 0.20 0.51 0.72 0.34 0.73 0.74 0.25
VARS2 3.2 CEU 10 7.30 0.69 10.78 0.86 1.43 0.89 0.09 0.24 0.65 0.40 0.73 0.74 0.25
HLA-DMB 3.1 CEU 14 10.60 0.91 12.12 0.89 0.45 0.66 0.30 -0.28 0.47 0.60 -0.050 0.54 0.51
PTPN22 3.5 CEU 7 4.70 0.44 4.57 0.41 -0.077 0.51 0.49 -0.98 0.23 0.80 -0.81 0.31 0.75
BAT3 2.0 CEU 3 3.47 0.21 3.14 0.27 -0.20 0.47 0.57 -0.35 0.46 0.64 -0.36 0.44 0.62
C6orf47 2.0 CEU 3 3.59 0.21 5.21 0.48 0.98 0.81 0.18 0.92 0.85 0.19 1.09 0.84 0.13
IL10 2.3 CEU 3 2.97 0.15 5.95 0.55 2.12 0.97 0.01 0.90 0.84 0.16 1.47 0.94 0.04
CDSN/ 4.5 CEU 59 30.80 >0.99 49.42 >0.99 2.17 0.97 0.01 1.40 0.95 0.03 1.98 0.97 0.01
PSORSC1                 
   YRI 63 32.88 >0.99 46.20 >0.99 1.46 0.99 0.01 1.44 >0.99 <0.01 1.72 >0.99 <0.01
   EAS 64 33.41 >0.99 47.50 >0.99 1.52 0.91 0.08 1.45 0.98 001 1.75 0.98 0.02
TRIM40/ 9.1 CEU 68 17.51 0.98 26.13 0.99 1.78 0.96 0.03 1.61 0.98 <0.01 1.98 0.97 <0.01
TRIM10                 
   YRI 64 16.48 0.96 15.74 0.94 -0.16 0.64 0.22 1.07 0.97 <0.01 0.76 0.93 0.02
   EAS 79 20.34 0.99 19.33 0.98 -0.18 0.46 0.31 -0.20 0.46 0.68 -0.23 0.45 0.71
BTNL2 3.8 CEU 53 33.04 >0.99 39.75 0.99 -0.33 0.42 0.36 1.32 0.93 0.03 0.88 0.78 0.15
   YRI 63 39.28 >0.99 30.01 >0.99 0.043 0.71 0.18 0.67 0.89 0.06 0.53 0.86 0.07
   EAS 94 58.60 >0.99 47.38 >0.99 -0.70 0.31 0.21 0.95 0.88 0.13 0.43 0.69 0.35
TAP2 4.4 CEU 33 17.56 0.98 29.07 0.99 2.27 0.98 0.01 1.59 0.98 0.01 2.16 0.98 <0.01
   YRI 54 28.73 >0.99 34.55 >0.99 0.73 0.94 0.05 1.63 >0.99 <0.01 1.56 0.99 <0.01
   EAS 41 21.81 0.99 32.88 >0.99 1.79 0.97 0.04 1.30 0.96 0.04 1.74 0.98 0.02
TAP2-ctr 2.6 CEU 12 10.71 0.91 12.18 0.89 0.42 0.65 0.32 0.46 0.70 0.29 0.52 0.69 0.18
BTNL2-ctr 2.0 CEU 15 17.47 0.98 16.73 0.96 -0.14 0.50 0.54 1.56 0.97 0.01 1.18 0.90 0.09
  1. a length of analyzed sequenced region (kb);
  2. b sampled population (for each population 40 chromosomes were resequenced);
  3. c number of segregating sites;
  4. d Watterson's theta estimation per site (×10-4);
  5. e nucleotide diversity per site (×10-4);
  6. f percentile rank relative to a distribution of 238 5kb segments from NIEHS genes;
  7. g p value applying demographic coalescent simulations.