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

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

Structure of myristoyl dihydrosphingomyelin (d18:0/14:0)*
Metabolite Accession: GCST90200049
Name: myristoyl dihydrosphingomyelin (d18:0/14:0)*
Hmdb Id: HMDB0012085
Super Pathway: NA
Sub Pathway: NA
Inchikey: MJAFYELZQYPMQG

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):
-0.257
Position:
12973521
SE (Ratio):
0.018
Effect Allele:
A
Z-score (Ratio):
-14.598
Reference Allele:
T
-log10(P):
-109.469
MAF:
0.387
Beta (Num):
-0.075
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.182
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 de novo biosynthesis, Sphingomyelin metabolism.6[1], 7[2], 8[3], 9[4]

Denominator Metabolite Explanation:

Sphingolipid de novo biosynthesis.7[1], 8[2], 10[3], 11[4], 12[5]

Ratio Explanation:

The ratio reflects sphingolipid maturation, comparing a downstream product (sphingomyelin) to an early precursor (dihydrosphingomyelin), potentially indicating ceramide desaturase activity.13[1], 12[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

ISM1 is linked to cholelithiasis and influences lipid metabolism, including LDL cholesterol, which mediates the protective effect of sphingomyelin on gallstone formation.14[1], 15[2], 16[3], 17[4] The ratio may reflect altered sphingolipid metabolism associated with cholelithiasis.18[5], 19[6], 20[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