lignoceroyl sphingomyelin (d18:1/24:0) to sphingomyelin (d18:1/14:0, d16:1/16:0)*

Numerator Metabolite

Structure of lignoceroyl sphingomyelin (d18:1/24:0)
Metabolite Accession: GCST90200020
Name: lignoceroyl sphingomyelin (d18:1/24:0)
Hmdb Id: HMDB0011697
Super Pathway: NA
Sub Pathway: NA
Inchikey: QEDPUVGSSDPBMD

Denominator Metabolite

Structure of sphingomyelin (d18:1/14:0, d16:1/16:0)*
Metabolite Accession: GCST90199945
Name: sphingomyelin (d18:1/14:0, d16:1/16:0)*
Hmdb Id: HMDB0012097
Super Pathway: NA
Sub Pathway: NA
Inchikey: KYICBZWZQPCUMO

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):
-0.212
Position:
12959398
SE (Ratio):
0.017
Effect Allele:
T
Z-score (Ratio):
-12.558
Reference Allele:
C
-log10(P):
-81.614
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.118
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.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2], 6[3]

Ratio Explanation:

The ratio compares a very-long-chain sphingomyelin to shorter-chain species, both part of the sphingolipid metabolism pathway regulated by factors including ISM1.1[1], 4[2], 2[3]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Lower ISM1 function may alter sphingolipid metabolism, impacting the ratio of very-long to shorter-chain sphingomyelins.1[1], 2[2], 7[3], 8[4] This dysregulation is linked to altered LDL cholesterol levels and an increased risk of cholelithiasis.7[5], 9[6], 8[7]

Phenotype Driver:

Metabolite-centric:lignoceroyl sphingomyelin (d18:1/24:0) to sphingomyelin (d18:1/14:0, d16:1/16:0)*

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