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

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

Metabolite Accession: GCST90200013
Name: sphingomyelin (d18:1/22:2, d18:2/22:1, d16:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs4814175

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):
-0.167
Position:
12959094
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-10.164
Reference Allele:
T
-log10(P):
-54.206
MAF:
0.387
Beta (Num):
-0.048
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.119
SE (Den):
0.014
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.5[1], 6[2], 7[3]

Ratio Explanation:

This ratio may reflect altered sphingomyelin acyl chain composition, potentially influenced by ISM1's role in lipid metabolism, though a direct enzymatic link is not established.1[1], 2[2]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Elevated ISM1 levels are linked to cholelithiasis.3[1], 8[2], 9[3] ISM1 influences lipid metabolism, which may alter bile composition, increasing gallstone risk.1[4], 2[5], 10[6] The sphingomyelin ratio likely reflects this altered lipid environment, which is also associated with changes in LDL-cholesterol and ALT.11[7], 12[8]

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