lignoceroyl sphingomyelin (d18:1/24:0) to sphingomyelin (d18:1/20:0, d16:1/22:0)*

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 (d18:1/20:0, d16:1/22:0)*
Metabolite Accession: GCST90200001
Name: sphingomyelin (d18:1/20:0, d16:1/22:0)*
Hmdb Id: HMDB0012102
Super Pathway: NA
Sub Pathway: NA
Inchikey: AADLTHQNYQJHQV

Associated Genomic Regions

Region: rs12897637

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
-0.363
Position:
64239351
SE (Ratio):
0.019
Effect Allele:
C
Z-score (Ratio):
-18.874
Reference Allele:
T
-log10(P):
-181.275
MAF:
0.165
Beta (Num):
-0.066
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
0.297
SE (Den):
0.020
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs1871194

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.230
Position:
8283819
SE (Ratio):
0.015
Effect Allele:
C
Z-score (Ratio):
15.142
Reference Allele:
A
-log10(P):
-117.586
MAF:
0.462
Beta (Num):
0.029
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.201
SE (Den):
0.016
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

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):
-0.274
Position:
12959398
SE (Ratio):
0.015
Effect Allele:
T
Z-score (Ratio):
-18.502
Reference Allele:
C
-log10(P):
-174.300
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.180
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.3[1], 4[2]

Denominator Metabolite Explanation:

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

Ratio Explanation:

This ratio reflects ceramide synthase (CERS) activity, where CERS4 influences the numerator (C24:0) precursor, altering the balance between different sphingomyelin species.2[1]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CERS4 variation alters sphingolipid composition, impacting lipid metabolism. This dyslipidemia is associated with cholelithiasis (gallstones), disorders of lipoprotein metabolism, and gout, all phenotypes linked to systemic metabolic disturbances and inflammation.5[1], 6[2], 7[3], 8[4]

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