sphingomyelin (d18:2/24:1, d18:1/24:2)* to sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*

Numerator Metabolite

Metabolite Accession: GCST90200040
Name: sphingomyelin (d18:2/24:1, d18:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Structure of sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Metabolite Accession: GCST90200017
Name: sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: LQINJRUGTUOHGS

Associated Genomic Regions

Region: rs364585

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):
-0.151
Position:
12962718
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-9.470
Reference Allele:
G
-log10(P):
-47.321
MAF:
0.384
Beta (Num):
-0.068
Novel Locus:
Yes ✔️
SE (Num):
0.014
Beta (Den):
0.083
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 and degradation.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingomyelin biosynthesis and degradation.4[1], 5[2], 6[3]

Ratio Explanation:

The ratio reflects alterations in sphingomyelin metabolism, potentially influenced by ISM1's role in overall lipid homeostasis, though a direct enzymatic link is not established.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1 may influence the risk of cholelithiasis by modulating hepatic lipid metabolism, including sphingomyelins and cholesterol, which in turn affects bile composition and gallstone formation.1[1], 7[2], 2[3], 3[4]

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