stearoyl sphingomyelin (d18:1/18:0) to sphingomyelin (d18:2/24:1, d18:1/24:2)*

Numerator Metabolite

Structure of stearoyl sphingomyelin (d18:1/18:0)
Metabolite Accession: GCST90200335
Name: stearoyl sphingomyelin (d18:1/18:0)
Hmdb Id: HMDB0001348
Super Pathway: NA
Sub Pathway: NA
Inchikey: LKQLRGMMMAHREN

Denominator Metabolite

Metabolite Accession: GCST90200040
Name: sphingomyelin (d18:2/24:1, d18:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs1466448

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
-0.305
Position:
8289519
SE (Ratio):
0.020
Effect Allele:
C
Z-score (Ratio):
-15.542
Reference Allele:
A
-log10(P):
-123.755
MAF:
0.191
Beta (Num):
-0.230
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
0.075
SE (Den):
0.018
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs364585

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
0.160
Position:
12962718
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
10.001
Reference Allele:
G
-log10(P):
-52.547
MAF:
0.384
Beta (Num):
0.092
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
-0.068
SE (Den):
0.014
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]

Denominator Metabolite Explanation:

Sphingolipid metabolism.6[1], 7[2]

Ratio Explanation:

The ratio reflects the activity of ceramide synthase CERS4, influencing the balance between different sphingomyelin species which can impact membrane composition and cell signaling.8[1]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CERS4's role in sphingolipid metabolism influences the composition of sphingomyelins.8[1], 9[2] Altered sphingomyelin levels are associated with cholelithiasis and changes in LDL-cholesterol and ALT levels, suggesting a link between CERS4 activity, this metabolic ratio, and the observed phenotypes.10[3], 11[4], 12[5], 13[6]

Phenotype Driver:

Gene-centric:CERS4

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