n-palmitoyl-sphingosine (d18:1/16:0) to sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*

Numerator Metabolite

Structure of n-palmitoyl-sphingosine (d18:1/16:0)
Metabolite Accession: GCST90200336
Name: n-palmitoyl-sphingosine (d18:1/16:0)
Hmdb Id: HMDB0004949
Super Pathway: NA
Sub Pathway: NA
Inchikey: YDNKGFDKKRUKPY

Denominator Metabolite

Structure of sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Metabolite Accession: GCST90200010
Name: sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Hmdb Id: HMDB0012104
Super Pathway: NA
Sub Pathway: NA
Inchikey: VBFKEZGCUWHGSK

Associated Genomic Regions

Region: rs964184

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
0.206
Position:
116648917
SE (Ratio):
0.025
Effect Allele:
G
Z-score (Ratio):
8.194
Reference Allele:
C
-log10(P):
-35.918
MAF:
0.131
Beta (Num):
0.132
Novel Locus:
Yes ✔️
SE (Num):
0.023
Beta (Den):
-0.074
SE (Den):
0.021
No CNV overlap
rQTL cluster:
248
Reaction Distance:
NA
Closest Genes:
ZNF259 BUD13 APOA5 APOA4 APOC3

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid de novo biosynthesis4[1], 5[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism6[1], 7[2]

Ratio Explanation:

The ratio reflects the balance between ceramide (numerator) and sphingomyelin (denominator), two key lipids transported by lipoproteins whose metabolism is influenced by apolipoproteins.8[1], 9[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Variants in the APOA1/A4/A5/C3 gene cluster alter apolipoprotein function, leading to dysregulated lipoprotein and sphingolipid metabolism, which is reflected in the ratio.8[1], 2[2] This dyslipidemia is a primary cause of associated cardiovascular phenotypes like hypercholesterolemia and atherosclerosis.3[3], 10[4]

Phenotype Driver:

Gene-centric:APOA1/A4/A5/C3 cluster

Downloads

Download the full rQTL summary statistics file for this metabolite ratio. Data contains the loci listed here. For each SNP (chromosome, effect_allele, reference_allele, pos_name, position) these columns contain the summary statistics of the ratio (beta, pgain, pval, se, z), the numerator metabolite (beta_1, pval_1, n_iids_1, effect_allele_frequency_1, se_1, z_1) and the denominator metabolite (beta_2, pval_2, n_iids_2, effect_allele_frequency_2, se_2, z_2)

Download rQTL Data