sphingomyelin (d18:1/24:1, d18:2/24:0)* to sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*

Numerator Metabolite

Structure of sphingomyelin (d18:1/24:1, d18:2/24:0)*
Metabolite Accession: GCST90199972
Name: sphingomyelin (d18:1/24:1, d18:2/24:0)*
Hmdb Id: HMDB0012107
Super Pathway: NA
Sub Pathway: NA
Inchikey: WKZHECFHXLTOLJ

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: rs4814176

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:
20
Beta (Ratio):
-0.131
Position:
12959398
SE (Ratio):
0.016
Effect Allele:
T
Z-score (Ratio):
-8.117
Reference Allele:
C
-log10(P):
-35.280
MAF:
0.387
Beta (Num):
-0.048
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.083
SE (Den):
0.015
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid biosynthesis/metabolism

Denominator Metabolite Explanation:

Sphingolipid biosynthesis/metabolism

Ratio Explanation:

The ratio compares sphingomyelin species with very-long-chain fatty acids (VLCFA), C24, to those with C22 chains, potentially reflecting ceramide synthase or fatty acid elongase activity.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

A higher ratio of C24/C22 sphingomyelins, potentially influenced by ISM1's role in lipid metabolism, is associated with cholelithiasis (gallstones) and altered LDL-cholesterol and ALT levels.5[1], 6[2], 7[3]

Phenotype Driver:

Gene-centric:ISM1

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