n-palmitoyl-sphingosine (d18:1/16:0) to palmitoyl sphingomyelin (d18:1/16:0)

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 palmitoyl sphingomyelin (d18:1/16:0)
Metabolite Accession: GCST90199876
Name: palmitoyl sphingomyelin (d18:1/16:0)
Hmdb Id: HMDB0010169
Super Pathway: NA
Sub Pathway: NA
Inchikey: RWKUXQNLWDTSLO

Associated Genomic Regions

Region: rs964184

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

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
11
Beta (Ratio):
0.192
Position:
116648917
SE (Ratio):
0.023
Effect Allele:
G
Z-score (Ratio):
8.272
Reference Allele:
C
-log10(P):
-36.569
MAF:
0.131
Beta (Num):
0.132
Novel Locus:
Yes ✔️
SE (Num):
0.023
Beta (Den):
-0.060
SE (Den):
0.022
No CNV overlap
rQTL cluster:
248
Reaction Distance:
NA
Closest Genes:
ZNF259 BUD13 APOA5 APOA4 APOC3

LLM Analysis

Numerator Metabolite Explanation:

Ceramide biosynthesis, Sphingolipid metabolism.5[1], 6[2]

Denominator Metabolite Explanation:

Sphingomyelin biosynthesis, Sphingolipid metabolism.5[1], 7[2]

Ratio Explanation:

This ratio reflects sphingomyelin synthesis from ceramide, a key step in sphingolipid metabolism.8[1], 7[2], 9[3] Altered apolipoprotein function likely impacts the transport of these lipids.10[4]

Ratio Evidence:

canonical reaction, not mediated by an associated enzyme

Gene Ratio Phenotype Relationship:

Genetic variants in the APOA1/C3/A4/A5 cluster alter lipoprotein metabolism, influencing the balance of ceramide and sphingomyelin.1[1], 10[2], 2[3] This dysregulation is associated with an increased risk for hypercholesterolemia and a spectrum of atherosclerotic cardiovascular diseases, including myocardial infarction and atherosclerosis.11[4], 12[5], 13[6]

Phenotype Driver:

Gene-centric:APOA1/APOC3/APOA4/APOA5 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