sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)* to sphingomyelin (d18:2/18:1)*

Numerator Metabolite

Structure of sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Metabolite Accession: GCST90200017
Name: sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: LQINJRUGTUOHGS

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: 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):
0.138
Position:
12959094
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
8.750
Reference Allele:
T
-log10(P):
-40.685
MAF:
0.387
Beta (Num):
0.084
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
-0.054
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.5[1], 6[2], 7[3]

Denominator Metabolite Explanation:

Sphingolipid biosynthesis/metabolism.5[1], 6[2], 7[3]

Ratio Explanation:

The ratio reflects altered sphingolipid metabolism. ISM1, a gene associated with sphingolipid pathways, may influence the relative abundance of different sphingomyelin species.8[1], 3[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Genetic variation near ISM1 is linked to altered sphingolipid profiles.8[1], 3[2] Both sphingomyelin levels and ISM1 function are independently associated with cholelithiasis and lipid parameters like LDL-C and ALT, suggesting a complex gene-metabolite-phenotype interaction affecting liver and biliary health.9[3], 10[4], 11[5], 12[6], 13[7]

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