Comparative GWAS Analysis of Autoimmune Diseases

To avoid bias caused by the overlap of exposure and outcome samples, we obtained exposure and outcome samples from different databases. When selecting exposure and outcome GWAS datasets, European origin of population, more comprehensive disease type, larger size of population samples and SNPs, more comprehensive gender composition, and time of data publication were comprehensively taken into account. The GWAS dataset associated with SLE was established by European Bioinformatics Institute, with the ID number of “ebi-a-GCST003156”, and was comprised of 14,267 samples and 7,071,163 SNPs (https://gwas.mrcieu.ac.uk/). The GWAS datasets associated with thyroid diseases were established by FinnGen Biobank. The hyperthyroidism GWAS dataset was comprised of 173,938 samples and 16,380,189 SNPs with the ID numbers of “finn-b-AUTOIMMUNE_HYPERTHYROIDISM” and the hypothyroidism GWAS dataset was comprised of 213,990 samples and 16,380,461 SNPs, with the ID number of “finn-b-E4_HYTHYNAS” (https://gwas.mrcieu.ac.uk/). Details of the three GWAS datasets were listed in Supplementary Table 1.