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Official Journal of the Human Genome Organisation

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Table 6 Details of 8 SNPs in 7 Genes that showed significant cross-validated association with antibody response, and of other assayed SNPs in those genes that showed significant association in both half-samples

From: Genetic determinants of immune-response to a polysaccharide vaccine for typhoid

Gene Chromosome no. Total no. of SNPs assayeda No. of “significant” SNPs Details of “significant” SNPs r In half-sample 1 (n = 492)d r In half-sample 2 (n = 492)d P-value using PLINK in the total samplee (n = 984)
rs # nt Position SNP location within gene (mRNA transcript no. in NCBI database)
IL1RL1 2 13 3 4142132b 102303914 Intron 1 (NM_016232.4) 0.96 0.94 0.011
1997466b 102317899 Intron 1 (NM_016232.4) 0.91 0.94 0.016
10208293 c 102332742 Intron 10 (NM_016232.4) 0.95 0.91 0.002
CTLA4 2 1 1 231779 c 204442732 Intron 1 (NM_005214.3) −0.99 −0.93 0.028
CD86 3 17 1 17203439 c 123278196 Intron 1 (NM_175862.3) 0.95 0.97 0.016
TLR1 4 24 2 55815313b 38481645 Intron 2 (NM_003263.3) 0.95 0.94 0.022
5743572 c 38481786 Intron 2 (NM_003263.3) 0.98 0.93 0.050
DEFB1 8 33 7 2978873 c 6717373 Intron 1 (NM_005218.3) 0.98 0.98 0.016
2977780b 6717513 Intron 1 (NM_005218.3) 0.95 0.95 0.018
2980928b 6717829 Intron 1 (NM_005218.3) 0.95 0.95 0.018
2978872b 6718140 Intron 1 (NM_005218.3) 0.93 0.98 0.008
2951854b 6718836 Intron 1 (NM_005218.3) 0.92 0.94 0.028
2980923b 6720467 Intron 1 (NM_005218.3) 0.95 0.93 0.015
2977772 c 6720606 Intron 1 (NM_005218.3) 0.91 0.94 0.013
MAPK8 10 7 1 10857564 c 49282578 Intron 1 (NM_002750.2) −0.95 −0.96 0.030
IL17D 13 6 1 1888001 c 20183906 Intron 2 (NM_138284.1) 0.94 0.91 0.018
  1. aIncluding assayed SNPs in 2 kb regions upstream and downstream of the gene
  2. bAssociation significant in both Half-samples (was not included in the initial analysis of 469 SNPs)
  3. cAssociation found to be significant in Half-Sample 1 and cross-validated in Half-Sample 2 (i.e., included in the initial analysis of 469 SNPs)
  4. dP-values corresponding to these correlation coefficients are all <0.005, and with FDR < 0.05
  5. eEssentially each P-value corresponds to a test of equality of mean values of logAR among individuals belonging to the three genotypes at the locus under consideration