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

Numerator Metabolite

Metabolite Accession: GCST90200033
Name: sphingomyelin (d18:2/23:0, d18:1/23:1, d17:1/24:1)*
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: 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):
-0.138
Position:
12962718
SE (Ratio):
0.009
Effect Allele:
A
Z-score (Ratio):
-15.838
Reference Allele:
G
-log10(P):
-128.415
MAF:
0.384
Beta (Num):
0.016
Novel Locus:
No
SE (Num):
0.014
Beta (Den):
0.155
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 metabolism

Denominator Metabolite Explanation:

Sphingolipid metabolism

Ratio Explanation:

This ratio reflects altered de novo sphingolipid synthesis, where SPTLC3 variation likely modifies the fatty acid chain length composition of the resulting sphingomyelin species.1[1], 3[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variation in SPTLC3 alters sphingomyelin profiles.2[1], 4[2] This dysregulation of lipid metabolism affects bile composition and cholesterol solubility, increasing the risk for cholelithiasis, a colocalized phenotype that is also associated with LDL cholesterol levels.5[3], 6[4], 7[5]

Phenotype Driver:

Gene-centric:SPTLC3

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