Introduction Obesity roughly affects one third of adults in the United States and is often a precursor to various comorbidities, including diabetes, hypertension, and dyslipidemia. Studies have reported that ceramides, a precursor to complex sphingolipids, are increased in obese and diabetic patients and are drivers for metabolic disease. Previously published genome-wide association studies (GWAS) of circulating ceramides have identified reproducible associations with single nucleotide polymorphisms (SNPs) near the SPTLC3 gene. However, the functional consequences of these SNPs are unclear. Here, we aim to identify variants effecting the expression of SPTLC3, which may have a role in driving dysregulated ceramide levels. Methods We focused on SNPs that were genome-wide significant (p ≤ 5x10-8) from the National Human Genome Research Institute - European Bioinformatics Institute (NHGRI-EBI) GWAS catalog that are associated with various circulating ceramides and are within 100 kilo-base pairs of SPTLC3. Identified SNPs were examined for association with gene expression using the Genotype Tissue Expression Project (GTEx) and annotated with functional regulatory information from the Encyclopedia of DNA Elements (ENCODE). The RegulomeDB database was also used to annotate putative regulatory potential and identify predicted transcription factor binding motifs. After characterizing these SNPs, we designed and performed luciferase-based reporter assays for each SNP to determine their consequence on reporter activity. Results We identified 7 SNPs of interest that are associated with Cer(d18:1/18:0), Cer(d18:1/22:0), Cer(d18:1/24:0), Cer(d18:1/24:1), and Cer(d18:1/26:0) species. All SNPs are strong expression quantitative trait loci (eQTLs) for liver-specific expression of SPTLC3 (p ≤ 5.3x10-12), though, only two SNPs fall within candidate cis-regulatory elements from ENCODE. After performing luciferase-based reporter assays, we identified one SNP, rs4814175, that demonstrates reduced luciferase activity. This SNP has a predicted binding motif for transcription factors GATA2 and ALX1 and may be functionally important in regulating SPTLC3. Conclusion We identified rs4814175 as a potential driver for decreased SPTLC3 expression seen within human gene expression data. This SNP may impact binding of two potential transcription factors and may be a contributor to dysregulated circulating ceramides levels. Additional research is needed to fully understand the genetic drivers of ceramides.