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

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

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: rs12878001

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
-0.374
Position:
64239629
SE (Ratio):
0.020
Effect Allele:
G
Z-score (Ratio):
-18.815
Reference Allele:
T
-log10(P):
-180.157
MAF:
0.165
Beta (Num):
-0.066
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
0.308
SE (Den):
0.019
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs4814176

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.251
Position:
12959398
SE (Ratio):
0.015
Effect Allele:
T
Z-score (Ratio):
-16.339
Reference Allele:
C
-log10(P):
-136.507
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
No
SE (Num):
0.015
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:

Sphingolipid metabolism

Denominator Metabolite Explanation:

Sphingolipid metabolism

Ratio Explanation:

This ratio reflects the balance between a very-long-chain (C24:0) and other long-chain sphingomyelins.4[1], 5[2] Its alteration is linked to the regulatory protein ISM1.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1, a secreted protein, is associated with both the sphingomyelin ratio and lipid-related phenotypes.2[1], 3[2] Alterations in sphingomyelin composition, which are major components of lipoproteins, can impact lipoprotein metabolism and contribute to the risk of cholelithiasis and dyslipidaemia.6[3], 7[4], 8[5]

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