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

Numerator 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

Denominator 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

Associated Genomic Regions

Region: rs438568

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):
0.141
Position:
12958687
SE (Ratio):
0.015
Effect Allele:
A
Z-score (Ratio):
9.681
Reference Allele:
G
-log10(P):
-49.364
MAF:
0.384
Beta (Num):
0.087
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
-0.054
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 the balance between atypical odd-chain and common even-chain sphingomyelins, a process potentially modulated by the regulatory protein ISM1.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

The ISM1 gene likely regulates hepatic lipid metabolism, altering the balance of sphingomyelin species.1[1], 2[2] This may affect biliary cholesterol solubility, promoting cholelithiasis, and is also associated with changes in LDL-C and ALT levels.4[3], 5[4], 6[5], 7[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