sphingomyelin (d18:2/18:1)* to sphingomyelin (d18:1/19:0, d19:1/18:0)*

Numerator 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

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: rs364585

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):
-0.253
Position:
12962718
SE (Ratio):
0.015
Effect Allele:
A
Z-score (Ratio):
-16.641
Reference Allele:
G
-log10(P):
-141.507
MAF:
0.384
Beta (Num):
-0.054
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.199
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

Denominator Metabolite Explanation:

Sphingolipid biosynthesis

Ratio Explanation:

The ratio reflects the balance between different sphingomyelin species, which can be influenced by diet, metabolism, and genetic factors affecting lipid synthesis pathways.2[1], 3[2]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Genetic variants near ISM1, a gene involved in lipid metabolism, may alter the balance of sphingomyelin species.1[1] This altered ratio is associated with cholelithiasis (gallstones), potentially through ISM1's influence on lipid profiles, including LDL cholesterol, a known factor in gallstone formation.4[2], 5[3]

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