sphingomyelin (d18:2/16:0, d18:1/16:1)* to sphingomyelin (d18:1/21:0, d17:1/22:0, d16:1/23:0)*

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: GCST90200053
Name: sphingomyelin (d18:1/21:0, d17:1/22:0, d16:1/23:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

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):
-0.230
Position:
12958687
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-14.294
Reference Allele:
G
-log10(P):
-105.055
MAF:
0.384
Beta (Num):
-0.073
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.157
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 may reflect ISM1's influence on sphingomyelin acyl chain composition, potentially through indirect regulation of ceramide metabolism, a precursor for sphingomyelin synthesis.4[1], 3[2], 5[3]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1 may influence cholelithiasis risk and levels of LDL-C and ALT.6[1], 7[2] Altered sphingomyelin profiles are associated with cholelithiasis, and ISM1 levels are correlated with LDL-C and ALT, suggesting a gene-driven mechanism affecting lipid metabolism and liver function, which are linked to gallstone disease.6[3], 7[4], 8[5], 9[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