sphingomyelin (d18:2/24:1, d18:1/24:2)* to sphingomyelin (d18:1/21:0, d17:1/22:0, d16:1/23:0)*

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

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: rs4814176

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):
-0.224
Position:
12959398
SE (Ratio):
0.017
Effect Allele:
T
Z-score (Ratio):
-12.965
Reference Allele:
C
-log10(P):
-86.842
MAF:
0.386
Beta (Num):
-0.068
Novel Locus:
No
SE (Num):
0.014
Beta (Den):
0.156
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:

This ratio may reflect altered activity in the sphingomyelin biosynthesis pathway, potentially influenced by ISM1's role in lipid metabolism.6[1], 7[2], 3[3], 8[4]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1 is linked to cholelithiasis and influences lipid metabolism.1[1], 3[2], 9[3], 5[4], 10[5] An altered sphingomyelin ratio, a key component of bile and cell membranes, could affect bile composition and cholesterol solubility, contributing to gallstone formation and altered ALT and LDL-C levels.11[6], 12[7], 13[8]

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