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

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: GCST90200129
Name: sphingomyelin (d18:2/21:0, d16:2/23:0)*
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):
-0.139
Position:
12958687
SE (Ratio):
0.013
Effect Allele:
A
Z-score (Ratio):
-10.469
Reference Allele:
G
-log10(P):
-57.388
MAF:
0.384
Beta (Num):
-0.073
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.066
SE (Den):
0.013
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 reflects ceramide synthase activity, comparing sphingomyelins with C16 fatty acids to those with very-long-chain fatty acids, indicating altered sphingolipid metabolism.1[1], 4[2]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CERS4 and SPTLC3 influence the composition of sphingomyelin acyl chains.1[1], 5[2] Altered sphingolipid profiles are linked to cholelithiasis and dyslipidemia, potentially by affecting membrane properties and lipid metabolism in the liver, which is associated with gallstone formation and altered LDL-cholesterol levels.6[3], 7[4], 8[5]

Phenotype Driver:

Gene-centric:CERS4 1126-218-723-721-2788

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