In 2009 (i.e., before the discovery of IFNL4), results from genome wide association studies (GWAS) indicated that single-nucleotide polymorphisms (SNPs) lying near IFNL3 (rs12979860, rs8099917 and others) were strongly associated with response to pegylated interferon-α and ribavirin treatment for chronic hepatitis C,[6][7][8][9] as well as spontaneous clearance of hepatitis C (HCV) infection.

However, discovery of IFNL4 revealed that the rs12979860 SNP is located within intron 1 of IFNL4, while rs8099917 lies in an intergenic region, but nearest to IFNL4.

[5]  The rs12979860 and rs8099917 SNPs are in high linkage disequilibrium with a variant of IFNL4 (IFNL4-ΔG/TT; rs368234815) that controls generation of the IFNL4 protein.

[5] IFNL4-ΔG/TT appears to be the functional polymorphism that accounts for GWAS associations of nearby SNPs with HCV clearance, and IFNL4-ΔG/TT was shown to have stronger statistical association with HCV clearance than that of rs12979860, especially in populations of African ancestry in which linkage disequilibrium between these variants is weaker than in other populations.

[5][14] One possible functional variant in IFNL3 is the rs4803217 SNP, which lies in the 3’ untranslated regulatory region.