sphingomyelin (d18:1/20:0, d16:1/22:0)* to sphingomyelin (d18:2/18:1)*

Numerator Metabolite

Structure of sphingomyelin (d18:1/20:0, d16:1/22:0)*
Metabolite Accession: GCST90200001
Name: sphingomyelin (d18:1/20:0, d16:1/22:0)*
Hmdb Id: HMDB0012102
Super Pathway: NA
Sub Pathway: NA
Inchikey: AADLTHQNYQJHQV

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: 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):
0.234
Position:
12959094
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
13.544
Reference Allele:
T
-log10(P):
-94.551
MAF:
0.387
Beta (Num):
0.180
Novel Locus:
No
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:

Sphingolipid synthesis

Denominator Metabolite Explanation:

Sphingolipid synthesis

Ratio Explanation:

The ratio reflects altered sphingomyelin composition, potentially due to ISM1's influence on lipid metabolism, favoring sphingomyelins with saturated/monounsaturated very-long-chain fatty acids over polyunsaturated ones.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1's regulation of lipid metabolism likely alters sphingomyelin profiles, contributing to cholelithiasis. Studies show sphingomyelin has a protective effect against cholelithiasis, an effect mediated by LDL.3[1], 4[2] Elevated ALT and LDL-C are also associated with ISM1 and altered sphingolipid metabolism, indicating a link to liver dysfunction.5[3], 6[4], 7[5]

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