TABLE 3.
Top genome-wide-associated loci from the unadjusted analyses for Shigella-associated diarrheaa
| SNP | Ancestral:variant nucleotides | Nearest gene(s) | PROVIDE cohort |
CBC cohort |
Meta-analysis |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OR | MAF | No. of cases (n00, n01, n11) | No. of controls (n00, n01, n11) | P value | OR | MAF | No. of cases (n00, n01, n11 | No. of controls (n00, n01, n11) | P value | OR | P value | Het. P value | |||
| rs582240 | C:T | KRT18P59 | 0.45 | 0.29 | 64, 26, 3 | 146, 167, 23 | 3.91 × 10−5 | 0.37 | 0.31 | 33, 16, 1 | 42, 54, 14 | 5.06 × 10−4 | 0.43 | 6.40 × 10−8 | 0.69 |
| rs653552 | A:G | RP11-687M24.4 | 0.45 | 0.29 | 64, 26, 3 | 146, 167, 23 | 4.31 × 10−5 | 0.37 | 0.31 | 33, 16, 1 | 42, 54, 14 | 5.02 × 10−4 | 0.43 | 6.87 × 10−8 | 0.68 |
| rs147975801 | AATAC:A | KRT18P59, RP11-687M24.4 | 0.45 | 0.29 | 64, 26, 3 | 146, 167, 23 | 4.35 × 10−5 | 0.37 | 0.31 | 33, 16, 1 | 42, 54, 14 | 5.03 × 10−4 | 0.43 | 6.93 × 10−8 | 0.68 |
| rs12550437 | G:A | RP11-115J16.1 | 0.48 | 0.38 | 52, 35, 6 | 116, 165, 56 | 6.00 × 10−5 | 0.40 | 0.39 | 28, 19, 3 | 34, 52, 24 | 6.81 × 10−4 | 0.48 | 1.49 × 10−7 | 0.65 |
| rs10266841 | C:G | CYTH3 | 0.46 | 0.45 | 42, 44, 7 | 80, 180, 76 | 3.26 × 10−6 | 0.68 | 0.38 | 23, 22, 5 | 32, 66, 12 | 0.10 | 0.49 | 1.22 × 10−6 | 0.32 |
| rs2801847 | A:G | MPP7 | 2.68 | 0.07 | 66, 23, 0 | 300, 35, 1 | 5.87 × 10−5 | 2.12 | 0.07 | 40, 10, 0 | 99, 11, 0 | 0.08 | 3.55 | 1.11 × 10−5 | 0.54 |
a
Independent variants, their location, overlapping or nearest genes, genotype frequencies (accounting for dosage), and cohort-specific and meta-analyzed allelic odds ratios and statistical significances are presented. OR, allelic odds ratio; MAF, minor allele frequency; SNP, single nucleotide polymorphism; n00, number of infants homozygous for the ancestral allele; n01, number of infants heterozygous for the variant allele; n11, number of infants homozygous for the variant allele; Het. P value, heterozygosity P value.