Variant 3 (v3) is in near perfect linkage disequilibrium with v311 but it occurs less frequently that v311.
For each marker in the interaction for the formamide phenotype, there is a corresponding marker in near perfect linkage in the interaction for the indoleacetic acid phenotype.
One other SNP, in near perfect linkage disequilibrium, in the same gene (rs1544410) demonstrated a near significant effect in a random effects pooled analysis of Japanese, Thai, and Indian populations (OR: 0.77; 95% CI, 0.54 1.09) with moderate heterogeneity (I = 45.9%).
Two of the studies provided further data on rs20563 and rs20558, 2 missense SNPs in near perfect linkage disequilibrium, but again with nonsignificant pooled effects (both OR, 1.12; 95% CI, 0.92 1.38) and no heterogeneity.
These SNPs are in near complete linkage disequilibrium (LD; D′=0.99; R=0.94) in the GWAS population and so were considered as a single region of variation, represented by rs4253238 for the remainder of this study.
We could infer genotypes at Pro2008Ser in NCOR2 however as this variant was found to be in near perfect linkage disequilibrium (i.e. r2 = 1) with Ala2007Thr (determined based on sequencing of 69 84 individuals from each of the 5 populations).
We confirmed that rs4343, is in near perfect linkage disequilibrium (D'=1, r =0.88, n=64) with ACE I/D in Europeans (A and G alleles of rs4343 marking insertion and deletion alleles of ACE I/D respectively).
It is important that estimates of both the gene-risk factor and the gene-outcome associations are available for each of these variants, or for proxies of the variants (a proxy is a variant in complete or near complete linkage disequilibrium with the original variant).
1; in near-complete linkage disequilibrium with SNP rs2641348 in the ADAM30 gene [22]), SNP rs1153188 nearest (5'-flanking) to the DCD gene (chr. 12), SNP rs9472138 nearest (3'-flanking) to the VEGFA gene (chr. 6), and SNP rs10490072 nearest (3'-flanking) to the BCL11A gene (chr. 2).
In terms of copy number alone, we expect perfect or near-perfect linkage disequilibrium among those loci.
