sphingomyelin (d18:1/14:0, d16:1/16:0)* to sphingomyelin (d18:2/16:0, d18:1/16:1)*

Numerator Metabolite

Structure of sphingomyelin (d18:1/14:0, d16:1/16:0)*
Metabolite Accession: GCST90199945
Name: sphingomyelin (d18:1/14:0, d16:1/16:0)*
Hmdb Id: HMDB0012097
Super Pathway: NA
Sub Pathway: NA
Inchikey: KYICBZWZQPCUMO

Denominator 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

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):
0.191
Position:
12959094
SE (Ratio):
0.015
Effect Allele:
A
Z-score (Ratio):
13.001
Reference Allele:
T
-log10(P):
-87.310
MAF:
0.387
Beta (Num):
0.118
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.073
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]

Denominator Metabolite Explanation:

Sphingolipid metabolism.4[1]

Ratio Explanation:

The ratio reflects variations in sphingomyelin species. While ISM1 is associated with sphingolipid-related phenotypes, there is no direct evidence that it catalyzes this specific ratio change.5[1], 4[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Elevated ISM1 is linked to higher LDL-cholesterol, ALT, and cholelithiasis.6[1], 7[2], 8[3] ISM1 influences lipid metabolism, and altered sphingomyelin profiles are associated with LDL levels and cholelithiasis, suggesting a gene-driven mechanism impacting lipid-related phenotypes.9[4], 2[5], 10[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