Figure 2: Locus plots corresponding to genome-wide significant and suggestive loci associating with kidney stone
From: Common and rare variants associated with kidney stones and biochemical traits
Logistic regression was used for association testing between sequence variants and disease, treating disease status as the response and genotype counts as covariates (a–d) For each plot, the −log10 P values, derived by logistic regression, (y axis) for the sequence variants are shown according to their chromosomal positions (x axis). The significant loci are at 1p36 (a), 5q35 (c), 21q22 (d) and suggestive locus at 3q21 (b). Orange sequence variant colour represent association values after adjusting for the leading variant. Estimated recombination rates are shown as pink lines and the genomic locations of genes at the locus are depicted in blue. The red solid line indicates the threshold for genome-wide statistical significance, which takes into account the effects of multiple testing (P=0.05/28.3 million=1.8 × 10−9). The red broken line indicates the significance threshold for claiming independence of the index varaint based on the number variants located within the LD block containing the index variant at each locus (ALPL; 0.05/1,625=3.1 × 10−5, CASR; 0.05/1,078=4.6 × 10−5, SLC34A1; 0.05/2,516=2.0 × 10−5, CLDN14; 0.05/1,993=2.5 × 10−5).
