lignoceroyl sphingomyelin (d18:1/24:0) to sphingomyelin (d18:2/23:1)*

Numerator Metabolite

Structure of lignoceroyl sphingomyelin (d18:1/24:0)
Metabolite Accession: GCST90200020
Name: lignoceroyl sphingomyelin (d18:1/24:0)
Hmdb Id: HMDB0011697
Super Pathway: NA
Sub Pathway: NA
Inchikey: QEDPUVGSSDPBMD

Denominator Metabolite

Structure of sphingomyelin (d18:2/23:1)*
Metabolite Accession: GCST90200126
Name: sphingomyelin (d18:2/23:1)*
Hmdb Id: HMDB0240668
Super Pathway: NA
Sub Pathway: NA
Inchikey: PUTLJICFLAOKRD

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):
-0.156
Position:
12973521
SE (Ratio):
0.019
Effect Allele:
A
Z-score (Ratio):
-8.408
Reference Allele:
T
-log10(P):
-37.713
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.061
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 synthesis/metabolism.6[1], 7[2], 8[3]

Denominator Metabolite Explanation:

Sphingolipid synthesis/metabolism.6[1], 7[2], 8[3]

Ratio Explanation:

The ratio reflects the balance between two sphingomyelin species, which can be influenced by ISM1's role in overall lipid and cholesterol metabolism regulation.1[1], 4[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1 dysregulation alters lipid metabolism, including sphingomyelins, which are linked to LDL-cholesterol transport and bile composition.9[1], 1[2], 10[3] This metabolic shift is associated with an increased risk for cholelithiasis and elevated LDL-C and ALT.1[4], 10[5], 11[6]

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