Table 4

Sample set-specific haplotype association analysis at haplotype blocks 1 to 3
East Polynesian (High)b East Polynesian (Low)c West Polynesian East/West Polynesian European Caucasian
Hapa Freq. ORd (95% CI) Pd Freq. ORd (95% CI) Pd Freq. ORd (95% CI) Pd Freq. ORd (95% CI) Pd Freq. ORd (95% CI) Pd
Case Con Case Con Case Con Case Con Case Con
Block 1 (rs475414|rs17299124)
C|C 0.437 0.472 0.86 0.321 0.434 0.397 1.00 0.988 0.598 0.595 0.94 0.745 0.500 0.579 0.75 0.648 0.430 0.450 0.93 0.471
(0.63,1.16) (0.61,1.62) (0.67,1.34) (0.22,2.60) (0.76,1.14)
T|A 0.024 0.051 0.35 0.017 0.179 0.203 0.81 0.525 0.004 0.044 0.12 0.009 0.026 0.053 0.33 0.461 0.262 0.245 1.10 0.393
(0.15,0.83) (0.42,1.56) (0.03,0.59) (0.02,6.19) (0.88,1.38)
1.34 0.063 0.387 0.400 1.18 0.562 0.396 0.361 1.24 0.228 0.474 0.368 1.53 0.486 0.302 0.301 1.00 0.984
T|C 0.539 0.477 (0.98,1.82) (0.67,2.09) (0.88,1.76) (0.46,5.08) (0.80,1.24)
Block 2 (rs693591|rs17300741|rs2078267)
C|A|C 0.525 0.458 1.38 0.047 0.315 0.298 1.05 0.849 0.373 0.371 1.02 0.933 0.528 0.283 3.49 0.063 0.139 0.134 0.95 0.698
(1.00,1.90) (0.63,1.77) (0.72,1.43) (0.93,13.01) (0.72,1.25)
G|A|C 0.299 0.350 0.77 0.136 0.287 0.272 1.13 0.654 0.436 0.461 0.83 0.288 0.278 0.478 0.38 0.106 0.329 0.302 1.07 0.543
(0.54,1.09) (0.66,1.95) (0.60,1.17) (0.12,1.23) (0.87,1.32)
G|G|C 0.11 0.102 1.09 0.734 0.046 0.040 0.94 0.914 0.17 0.121 1.72 0.032 0.111 0.13 0.76 0.758 , , , ,
(0.66,1.83) (0.28,3.14) (1.05,2.83) (0.14,4.30)
G|G|T 0.061 0.090 0.56 0.070 0.352 0.381 0.87 0.607 0.019 0.043 0.50 0.117 0.083 0.109 0.93 0.932 0.525 0.556 0.98 0.830
(0.30,1.05) (0.52,1.47) (0.21,1.19) (0.19,4.68) (0.81,1.18)
Block 3 (rs3825018|rs475688|rs7932775|rs476037|rs478607)
A|C|T|G|A 0.273 0.327 0.71 0.053 0.510 0.545 0.81 0.420 0.290 0.303 0.89 0.520 0.167 0.421 0.29 0.088 0.678 0.717 0.82 0.059
(0.50,1.01) (0.48,1.36) (0.61,1.28) (0.07,1.21) (0.67,1.01)
G|C|C|G|A 0.179 0.136 1.26 0.283 0.078 0.115 0.78 0.582 0.159 0.129 1.37 0.214 0.139 0.053 , 0.997 0.035 0.024 1.19 0.534
(0.83,1.93) (0.32,1.88) (0.83,2.26) (0.68,2.08)
G|C|C|G|G 0.116 0.108 1.14 0.599 0.039 0.038 0.82 0.767 0.142 0.114 1.54 0.100 0.111 0.105 1.71 0.659 , , , ,
(0.69,1.89) (0.23,2.98) (0.92,2.59) (0.16,18.73)
G|T|C|G|A 0.057 0.068 0.84 0.574 0.000 0.016 , 0.998 0.111 0.102 1.01 0.971 0.139 0.053 0.96 0.968 , , , ,
(0.46,1.55) (0.59,1.73) (0.14,6.67)
G|T|C|G|G 0.098 0.139 0.64 0.068 0.226 0.131 2.03 0.036 0.026 0.034 0.63 0.354 0.056 0.105 0.31 0.301 0.161 0.133 1.33 0.039
(0.40,1.03) (1.05,3.95) (0.24,1.68) (0.04,2.83) (1.01,1.75)
G|T|T|A|A 0.266 0.213 1.53 0.030 0.128 0.131 0.90 0.776 0.264 0.314 0.78 0.183 0.361 0.263 2.28 0.300 0.088 0.087 1.04 0.836
(1.04,2.24) (0.44,1.85) (0.55,1.12) (0.48,10.80) (0.74,1.44)

aHap, haplotypes listed in alphabetical order; those with a frequency <0.01 were excluded. bEast Polynesian (High), individuals with a STRUCTURE ancestry level ≥0.67. cEast Polynesian (Low), individuals with a STRUCTURE ancestry level <0.67. dOR, odds ratio (adjusted by sex); P: asymptomatic P-value. freq., frequency; Con, control.

Flynn et al.

Flynn et al. Arthritis Research & Therapy 2013 15:R220   doi:10.1186/ar4417

Open Data