sphingomyelin (d18:2/16:0, d18:1/16:1)* to sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0)

Numerator Metabolite

Metabolite Accession: GCST90199947
Name: sphingomyelin (d18:2/16:0, d18:1/16:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Metabolite Accession: GCST90200047
Name: sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0)
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):
-0.160
Position:
12962718
SE (Ratio):
0.015
Effect Allele:
A
Z-score (Ratio):
-10.416
Reference Allele:
G
-log10(P):
-56.820
MAF:
0.384
Beta (Num):
-0.074
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.086
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:

Sphingomyelin biosynthesis

Denominator Metabolite Explanation:

Sphingomyelin biosynthesis

Ratio Explanation:

The ratio reflects differences in sphingomyelin species, likely due to variations in fatty acid precursor availability or specificity of the synthesizing enzymes.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Elevated ISM1 levels are associated with increased LDL-cholesterol and ALT.3[1], 4[2] A protective effect of sphingomyelin on cholelithiasis has been identified, which is largely mediated by LDL.5[3], 6[4] Therefore, altered ISM1 activity may influence sphingomyelin composition and LDL levels, contributing to cholelithiasis risk.

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