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Table 1 Allele frequencies and association tests for SNPs in 5q31 cytokine cluster

From: Identification of a haplotype block in the 5q31 cytokine gene cluster associated with the susceptibility to severe malaria

SNP rs# Gene Allelic state Frequency of derived allele Association P value
Ancestral Derived Severe malaria Mild malaria Raw Permutation
rs162887 SLC22A4 C T 0.369 0.402 0.381 1.000
rs3792876 SLC22A4 C T 0.234 0.236 0.944 1.000
rs3792878 SLC22A4 G A 0.954 0.932 0.235 0.996
rs3805665 SLC22A4 G A 0.23 0.237 0.823 1.000
rs3805668 SLC22A4 G A 0.229 0.236 0.818 1.000
rs270608 SLC22A4 A G 0.338 0.379 0.328 1.000
rs270607 SLC22A4 C T 0.372 0.397 0.515 1.000
rs2073839 SLC22A4 C T 0.234 0.236 0.950 1.000
rs3828673 SLC22A4 G A 0.234 0.236 0.950 1.000
rs3792885 SLC22A4 A T 0.229 0.236 0.818 1.000
rs272842 SLC22A4 T C 0.348 0.299 0.181 0.985
rs3761659 SLC22A4 C G 0.234 0.236 0.950 1.000
rs3805673 SLC22A4 G A 0.228 0.237 0.771 1.000
rs273915 SLC22A4 G C 0.375 0.397 0.563 1.000
rs272887 SLC22A4 C T 0.372 0.397 0.515 1.000
rs273909 SLC22A4 T C 0.071 0.093 0.307 1.000
rs272879 SLC22A4 G C 0.344 0.297 0.201 0.992
rs272873 SLC22A4 C T 0.167 0.175 0.773 1.000
rs2306772 SLC22A4 G A 0.234 0.236 0.950 1.000
rs272867   C T 0.344 0.298 0.205 0.992
rs3788987 SLC22A5 G A 0.232 0.238 0.843 1.000
rs2631362 SLC22A5 T C 0.365 0.376 0.769 1.000
rs2631359 SLC22A5 G A 0.363 0.379 0.671 1.000
rs4646301 SLC22A5 G A 0.236 0.253 0.614 1.000
rs274571 SLC22A5 T C 0.365 0.379 0.719 1.000
rs2073642 SLC22A5 C T 0.241 0.254 0.707 1.000
rs183898 SLC22A5 G C 0.361 0.381 0.597 1.000
rs4646305 SLC22A5 G A 0.237 0.251 0.678 1.000
rs274559 SLC22A5 C T 0.348 0.299 0.181 0.985
rs274558 SLC22A5 C T 0.353 0.299 0.144 0.965
rs274554 SLC22A5 A G 0.837 0.887 0.059 0.748
rs274553 SLC22A5 G C 0.163 0.113 0.059 0.748
rs274551 SLC22A5 C T 0.161 0.113 0.072 0.804
rs274549 SLC22A5 G T 0.163 0.113 0.059 0.748
rs274547 SLC22A5 T A 0.839 0.887 0.072 0.804
rs2285673 LOC441108 C T 0.227 0.199 0.388 1.000
rs2269822 LOC441108 Cb T 0.282 0.281 1.000 1.000
rs3749834   C T 0.236 0.238 0.929 1.000
rs2070730 IRF1 C T 0.418 0.407 0.765 1.000
rs2070727 IRF1 G T 0.42 0.406 0.725 1.000
rs2070723 IRF1 C T 0.582 0.593 0.765 1.000
rs2070722 IRF1 G T 0.596 0.587 0.823 1.000
rs739718a   A G 0.257 0.261 0.903 1.000
rs2069812a IL5 T C 0.241 0.302 0.083 0.848
rs2299015 RAD50 A C 0.111 0.186 0.008 0.193
rs2299014 RAD50 T G 0.074 0.07 0.838 1.000
rs2243677 RAD50 G A 0.887 0.804 0.004 0.107
rs2522414 RAD50 G C 0.887 0.804 0.004 0.107
rs2299013 RAD50 Cc G 0.104 0.186 0.004 0.101
rs2252775 RAD50 A C 0.11 0.186 0.007 0.174
rs2522394 RAD50 A G 0.887 0.804 0.004 0.107
rs2245460 RAD50 A T 0.112 0.189 0.006 0.160
rs2301713 RAD50 T C 0.113 0.186 0.010 0.242
rs3798135 RAD50 G A 0.113 0.186 0.010 0.242
rs2237060 RAD50 A C 0.04 0.055 0.351 1.000
rs2074369 RAD50 C T 0.883 0.804 0.006 0.158
rs2240032 RAD50 C T 0.106 0.183 0.006 0.152
rs1881457 IL13 A C 0.124 0.219 0.002 0.046d
rs1800925 IL13 T C 0.894 0.826 0.014 0.296
rs2066960 IL13 A C 0.628 0.636 0.830 1.000
rs20541a IL13 C T 0.33 0.389 0.115 0.924
rs2070874 IL4 T C 0.273 0.274 0.975 1.000
rs2243270 IL4 G A 0.263 0.266 0.913 1.000
rs2243289 IL4 A G 0.729 0.736 0.825 1.000
rs1468215 KIF3A T A 0.26 0.247 0.725 1.000
rs3798132 KIF3A A G 0.352 0.336 0.685 1.000
rs3798130 KIF3A G A 0.671 0.677 0.882 1.000
rs2299007 KIF3A T C 0.383 0.431 0.219 0.994
rs2237057 KIF3A T C 0.742 0.75 0.818 1.000
rs2299006 KIF3A G C 0.654 0.667 0.738 1.000
rs2299005 KIF3A T C 0.661 0.668 0.836 1.000
rs3798129 KIF3A A T 0.336 0.337 0.975 1.000
rs3756754 KIF3A C T 0.022 0.013 0.366 1.000
rs256871 SEPT8 C T 0.609 0.635 0.490 1.000
rs30534 SEPT8 G A 0.391 0.365 0.490 1.000
rs30533 SEPT8 T C 0.386 0.371 0.686 1.000
rs39588 SEPT8 C G 0.383 0.369 0.717 1.000
rs256875 SEPT8 T C 0.385 0.379 0.888 1.000
rs392916 SEPT8 T A 0.532 0.561 0.459 1.000
rs30527 SEPT8 C T 0.62 0.639 0.620 1.000
rs30524 SEPT8 G T 0.383 0.362 0.573 1.000
rs757537 ANKRD43 T C 0.131 0.157 0.357 1.000
  1. a SNP genotyped by TaqMan assay.
  2. b Allelic state could not be inferred.
  3. c Allelic state inferred based on the sequence of rhesus macaque.
  4. d Permutation P value < 0.05.
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