stearoyl sphingomyelin (d18:1/18:0) to sphingomyelin (d18:2/18:1)*

Numerator Metabolite

Structure of stearoyl sphingomyelin (d18:1/18:0)
Metabolite Accession: GCST90200335
Name: stearoyl sphingomyelin (d18:1/18:0)
Hmdb Id: HMDB0001348
Super Pathway: NA
Sub Pathway: NA
Inchikey: LKQLRGMMMAHREN

Denominator Metabolite

Structure of sphingomyelin (d18:2/18:1)*
Metabolite Accession: GCST90200128
Name: sphingomyelin (d18:2/18:1)*
Hmdb Id: HMDB0001348
Super Pathway: NA
Sub Pathway: NA
Inchikey: LKQLRGMMMAHREN

Associated Genomic Regions

Region: rs686548

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):
0.147
Position:
12973521
SE (Ratio):
0.015
Effect Allele:
A
Z-score (Ratio):
9.488
Reference Allele:
T
-log10(P):
-47.502
MAF:
0.386
Beta (Num):
0.092
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
-0.055
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 metabolism.5[1], 6[2], 7[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism.8[1], 9[2], 10[3], 11[4]

Ratio Explanation:

The ratio reflects the balance between two specific sphingomyelin species, which may be influenced by ISM1 and could indicate alterations in sphingolipid pathways.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Elevated ISM1 levels are associated with increased LDL-cholesterol and ALT, and a higher risk for cholelithiasis.1[1], 2[2] The altered sphingomyelin ratio may reflect ISM1's impact on lipid metabolism, contributing to the pro-lithogenic environment and liver stress indicated by the associated phenotypes.12[3], 13[4]

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