The regional association plot for the GWS indel on chromosome 5 (chr5:141988181, mapped to rs527904740) is presented in Supplemental Figure S2A. The next most significantly associated variant, rs74911483 (chr5:141990602, p=6.13E-8), is shown in Supplemental Figure S2B, and was in high LD with this variant (AFR: r2=0.87, D’=0.9454). Both variants were in the intron of the Fibroblast Growth Factor 1 (FGF1) gene. While FUMA could not be utilized for indel annotation, individual searches for the proxy SNP, rs74911483 in RegulomeDB55 (score of 5), Combined Annotation Dependent Depletion56 (maximum CADD score of 5), and GTEx57 (no eQTLs) did not provide persuasive support for regulatory effects of this variant. However, chromatin interactions were noted with neighboring genes (Supplemental Figure S3).
