palmitoyl sphingomyelin (d18:1/16:0) to 1-stearoyl-gpe (18:0)

Numerator 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

Denominator Metabolite

Structure of 1-stearoyl-gpe (18:0)
Metabolite Accession: GCST90199772
Name: 1-stearoyl-gpe (18:0)
Hmdb Id: HMDB0011130
Super Pathway: NA
Sub Pathway: NA
Inchikey: BBYWOYAFBUOUFP

Associated Genomic Regions

Region: rs1260326

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:
2
Beta (Ratio):
-0.173
Position:
27730940
SE (Ratio):
0.019
Effect Allele:
T
Z-score (Ratio):
-9.077
Reference Allele:
C
-log10(P):
-43.635
MAF:
0.413
Beta (Num):
-0.082
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.090
SE (Den):
0.015
No CNV overlap
rQTL cluster:
152
Reaction Distance:
NA
Closest Genes:
GCKR FNDC4 IFT172 AC109829.1 KRTCAP3

LLM Analysis

Numerator Metabolite Explanation:

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

Denominator Metabolite Explanation:

Glycerophospholipid metabolism.7[1], 8[2]

Ratio Explanation:

The ratio reflects lipoprotein particle composition, modulated by APOC1's influence on enzymes that remodel lipids and phospholipids on circulating lipoproteins.1[1], 4[2], 9[3], 10[4]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

APOC1 variants alter lipoprotein metabolism, reflected in the sphingomyelin to lysophospholipid ratio. This dysregulation of lipid transport contributes to hypercholesterolemia, atherosclerosis (myocardial infarction), and related metabolic disorders like Type 2 diabetes and cholelithiasis.1[1], 4[2], 11[3], 12[4]

Phenotype Driver:

Gene-centric:APOC1

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