Extended Data Table 2 AITD lead variants that are top cis-eQTL variants or correlated with top cis-eQTLs

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

  1. The AITD lead variants are as shown in Extended Data Table 1. The eQTL data was based on RNA-sequencing data from 13,173 Icelandic individuals who have provided whole-blood samples and from 686 who provided adipose tissue (see Methods). Association between sequence variants and gene expression (cis-eQTL) was estimated using a generalized linear regression, assuming additive genetic effects and quantile-normalized gene-expression estimates, adjusting for measurements of sequencing artefacts, demography variables and hidden covariates. We tested whether lead sequence variants associated with AITD were in strong LD (r2 > 0.8) with top cis-eQTL variants for genes expressed in whole blood and adipose tissue. Variants in LD with the lead variants at the novel loci were identified based on in-house genotype data using r2 > 0.8 for pairwise comparison of the nearest 100,000 variants to define an LD class. We only show eQTL variants that ranked top among all eQTL variants found for a given gene by stepwise conditional association testing.
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