Extended Data Table 1 Sequence variants associated with AITD in GWAS meta-analysis

From: FLT3 stop mutation increases FLT3 ligand level and risk of autoimmune thyroid disease

  1. We used logistic regression analysis assuming a multiplicative model, reporting ORs and two-sided P values adjusted for year of birth, sex and origin (Iceland; 4,692 cases and 342,061 controls) or the first 40 principal components (the UK Biobank; 25,542 cases and 383,111 controls). Variants were split into five classes based on their genome annotation, and the significance threshold based on the number of variants in each class (Methods). The primary signal at each locus was selected based on conditional association analysis of variants within 500 kb of the primary signal at each locus, using Bonferroni corrected P values based on those thresholds, and when plausible, we report the coding signal when two markers are equivalent after conditional analysis.
  2. *Uncorrelated secondary signals (based on conditional analysis) are presented with P values adjusted for primary signal (marker pairs: chromosome 2: 162,267,541 and chromosome 2: 162,268,127; chromosome 8: 128,144,770 and chromosome 8:128,557,125; chromosome 8: 132,908,273 and chromosome 8: 133,200,409; chromosome 10: 62,020,112 and chromosome 10: 62,245,825; and chromosome 12: 9,680,928 with chromosome 12: 9,683,329 and chromosome 12: 9,736,046).
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