Error from lead SNPs and candidate SNPs identification / No significant SNPs were identified.
This error can occur when no candidate SNPs are identified. Note that indels are included in the FUMA from v1.3.0 but both alleles need to match exactly with the selected reference panel.
MHC region is also excluded by default.
If there is no significant hit at your defined P-value cutoff for lead SNPs and GWAS-tagged SNPs, you can try to use a less stringent P-value threshold or provide predefined lead SNPs.
If there are significant SNPs with very low minor allele frequency, try decreasing MAF threshold (default 0.01).
Manhattan plots and significant-top 10 SNPs in your input file are available from SNP2GENE.
Recently, there have been cases where there are candidate SNPs where pvalue <5e-8. However, the variant id indicated that it was in GRCh38 and didn't match with our database. An example of this can be seen here: https://groups.google.com/g/fuma-gwas-users/c/coB3sLR6wUM/m/SvP84zpMAAAJ
Best,
Tanya