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. 2011 Oct 1;204(7):1031–1037. doi: 10.1093/infdis/jir493

Table 2.

Results From the Primary Association Analyses Between Single-Nucleotide Polymorphisms (SNPs) and Risk of Neuroinvasive Disease in Patients Infected With the West Nile Virus

SNP Rank Chromosome Position Allele
 Frequency
 HWE OR (95% CI) P
1 2 Cases Controls
rs2066786a 1 4 38978423 T C 0.3869 0.4639 0.2952 0.6781 (.5675–.8101) .0000188
rs2298771a 2 2 166601033 C T 0.3571 0.3014 0.1659 1.469 (1.218–1.772) .0000587
rs25651a 3 15 88136791 T C 0.2857 0.3423 0.003926 0.685 (.5636–.8326) .0001444
rs11575302b 5 7 50575187 A G 0.01964 0.01105 1 3.825 (1.867–7.838) .0002469
rs2177336b 8 3 197001272 T C 0.1464 0.1989 0.1278 0.6659 (.5282–.8395) .0005802
rs7163367a 10 15 88061148 A T 0.3964 0.4584 0.7443 0.7349 (.6154–.8777) .0006718
rs10839601b 12 11 6696711 A G 0.1821 0.1484 0.6071 1.457 (1.163–1.824) .001052
rs3738573a 17 1 84636843 C G 0.3222 0.368 0.5295 0.7398 (.6170–.8869) .001129
rs3733890b 18 5 78457714 A G 0.2631 0.3193 0.5488 0.7293 (.6024–.8830) .001214
rs323347a 19 8 30825765 G A 0.1571 0.1974 0.2596 0.6853 (.5438–.8637) .001363
rs11652709c 22 17 53626092 C G 0.3527 0.2979 0.07428 1.335 (1.118–1.595) .00145
rs1805073b 23 5 78362505 C G 0.2562 0.3047 0.3995 0.7346 (.6071–.8889) .001519
rs2824721b 25 21 18591988 G A 0.2071 0.2484 0.02988 0.7123 (.5767–.8797) .001638
rs1058587b 26 19 18360421 G C 0.2816 0.2405 0.1822 1.368 (1.126–1.664) .001657
rs10778292a 27 12 102784416 C T 0.1179 0.1526 0.2576 0.6536 (.5010–.8527) .001722
rs5370b 29 6 12404240 T G 0.2429 0.1979 0.3086 1.387 (1.127–1.707) .002003
rs3816988a 30 15 60898791 C T 0.1986 0.1575 0.2685 1.423 (1.136–1.783) .002161
rs12371985b 32 12 93466790 A G 0.01518 0.03316 1 0.3779 (.2021–.7064) .002295
rs2288777b 33 5 150900300 G A 0.05446 0.07474 0.6419 0.5692 (.3958–.8186) .002369
rs794999b 34 3 12204014 A G 0.2839 0.2479 0.6635 1.351 (1.113–1.640) .002371
rs16826069b 35 1 39569641 G A 0.258 0.21 0.5573 1.369 (1.115–1.680) .002647
rs2278428b 36 19 60109865 C A 0.06071 0.08105 0.2701 0.5904 (.4183–.8333) .002725
rs2161468b 38 19 9949270 G C 0.4482 0.3868 0.632 1.301 (1.093–1.548) .003051
rs2270962a 39 10 102006033 T C 0.05714 0.07526 0.6462 0.5893 (.4152–.8363) .003071
rs2270915b 40 5 32822145 G A 0.2392 0.1986 0.2619 1.365 (1.111–1.678) .003095
rs4432013b 41 11 4687755 G A 0.1911 0.2174 0.634 0.7146 (.5718–.8931) .003141
rs1527014b 42 12 16288943 G A 0.03839 0.02789 0.03282 2.024 (1.267–3.235) .0032
rs13095016b 43 3 196999988 C G 0.1437 0.1811 0.8272 0.6977 (.5492–.8865) .003223
rs11079339b 44 17 53625440 G A 0.1607 0.1326 0.1565 1.423 (1.124–1.803) .003431
rs2236358b 47 1 226002384 A G 0.05446 0.03789 1 1.836 (1.219–2.764) .00361
rs6263b 48 7 50563393 C T 0.01071 0.02158 0.3566 0.3336 (.1592–.6989) .003623
rs2523421b 51 6 29498418 G A 0.1146 0.09259 0.07721 1.496 (1.136–1.969) .004082
rs11076256a 53 16 57309966 T C 0.09732 0.06789 0.795 1.585 (1.155–2.174) .004313
rs1128349b 54 7 72735589 T C 0.4304 0.4716 0.3625 0.7757 (.6515–.9235) .004326
rs7574414b 55 2 227952148 A G 0.1518 0.1289 0.4732 1.426 (1.116–1.822) .004548
rs2287939b 57 5 34034639 A G 0.2571 0.3011 0.316 0.7519 (.6172–.9158) .004606
rs2290182b 59 16 65171508 C T 0.09643 0.1279 0.243 0.6592 (.4931–.8813) .004909
rs7143633b 61 14 20619732 G C 0.1616 0.1328 0.6737 1.418 (1.111–1.810) .00505
rs3754274b 63 1 84640197 A G 0.271 0.3027 1 0.7602 (.6275–.9211) .005131
rs7591849b 64 2 159821126 G T 0.467 0.4168 0.9468 1.276 (1.076–1.514) .00514
rs11540407b 65 12 74186648 T C 0.2308 0.26 0.4003 0.7472 (.6088–.9171) .005299
rs9380006a 66 6 27764477 C A 0.1482 0.1747 0.1773 0.7209 (.5711–.9099) .005871
rs1047881b 75 1 211097780 C T 0.4768 0.4289 0.3896 1.271 (1.068–1.513) .006946
rs2241988a 89 3 57517212 T C 0.4786 0.4184 0.5941 1.261 (1.061–1.499) .008448
rs6046a 132 13 112821159 A G 0.1027 0.1221 0.8795 0.708 (.5396–.9291) .01275
rs2240154a 135 19 954171 T C 0.1759 0.1553 0.9019 1.337 (1.063–1.681) .01302
rs5748648a 259 22 15660821 A G 0.04286 0.06632 0.599 0.6385 (.4315–.9450) .02491

SNPs were selected to undergo replication as detailed below. Abbreviations: A, adenine; C, cytosine; CI, confidence interval; G, guanine; HWE, Hardy-Weinberg equilibrium; OR, odds ratio; T, thymine.

a

Selected for replication according to results from 445 case patients and 813 control patients.

b

Selected for replication according to results from the complete sample of case patients and control patients.

c

Selected for replication according to results from the complete sample of case patients and control patients but replaced with rs10853004 in the replication panels. Frequency estimates and ORs (along with their 95% CIs) are calculated with respect to allele 1. Also included are significance levels for tests of HWE.