sphingomyelin (d18:1/18:1, d18:2/18:0) to sphingomyelin (d18:2/21:0, d16:2/23:0)*

Numerator Metabolite

Structure of sphingomyelin (d18:1/18:1, d18:2/18:0)
Metabolite Accession: GCST90199878
Name: sphingomyelin (d18:1/18:1, d18:2/18:0)
Hmdb Id: HMDB0012101
Super Pathway: NA
Sub Pathway: NA
Inchikey: NBEADXWAAWCCDG

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: rs603424

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Clumped rQTL variant

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SNP Summary

Chr:
10
Beta (Ratio):
0.123
Position:
102075479
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
7.831
Reference Allele:
G
-log10(P):
-32.962
MAF:
0.176
Beta (Num):
0.078
Novel Locus:
Yes ✔️
SE (Num):
0.019
Beta (Den):
-0.045
SE (Den):
0.017
No CNV overlap
rQTL cluster:
67
Reaction Distance:
NA
Closest Genes:
PKD2L1 BLOC1S2 SCD CWF19L1 CHUK

Region: rs4814175

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.099
Position:
12959094
SE (Ratio):
0.012
Effect Allele:
A
Z-score (Ratio):
-8.024
Reference Allele:
T
-log10(P):
-34.518
MAF:
0.387
Beta (Num):
-0.033
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:

Sphingolipid metabolism, ceramide synthesis.2[1], 3[2], 4[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism, ceramide synthesis.2[1], 3[2], 4[3]

Ratio Explanation:

The ratio contrasts sphingomyelins with C18 acyl chains against those with very-long-chains, likely reflecting shifts in ceramide precursor synthesis regulated by ISM1.

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variation in ISM1 likely alters de novo sphingolipid synthesis, changing sphingomyelin profiles.1[1], 5[2] This dysregulation of lipid metabolism is strongly associated with increased risk for cholelithiasis, hypercholesterolaemia, and various forms of ischaemic heart disease.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