lignoceroyl sphingomyelin (d18:1/24:0) to sphingomyelin (d18:1/19:0, d19:1/18:0)*

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

Metabolite Accession: GCST90200131
Name: sphingomyelin (d18:1/19:0, d19:1/18:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

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):
-0.294
Position:
12959398
SE (Ratio):
0.019
Effect Allele:
T
Z-score (Ratio):
-15.747
Reference Allele:
C
-log10(P):
-126.974
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.200
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.4[1], 5[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2]

Ratio Explanation:

This ratio reflects the balance of very long-chain (C24:0) versus odd-chain (C19:0) sphingomyelins. ISM1's role in overall lipid metabolism may influence this balance.2[1]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

ISM1, a secreted protein with pQTL colocalization, influences lipid metabolism and is phenotypically associated with cholelithiasis, ALT, and LDL-C.1[1], 6[2], 7[3] Altered sphingolipid metabolism is also linked to gallstone formation, suggesting ISM1 may modulate this process and impact related liver and lipid markers.8[4], 9[5], 10[6], 11[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