sphingomyelin (d18:2/24:1, d18:1/24:2)* to sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*

Numerator 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

Denominator Metabolite

Structure of sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Metabolite Accession: GCST90200010
Name: sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1)*
Hmdb Id: HMDB0012104
Super Pathway: NA
Sub Pathway: NA
Inchikey: VBFKEZGCUWHGSK

Associated Genomic Regions

Region: rs35372182

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
-0.210
Position:
64236157
SE (Ratio):
0.017
Effect Allele:
G
Z-score (Ratio):
-12.465
Reference Allele:
A
-log10(P):
-80.437
MAF:
0.166
Beta (Num):
-0.005
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
0.206
SE (Den):
0.019
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

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):
-0.151
Position:
12959398
SE (Ratio):
0.013
Effect Allele:
T
Z-score (Ratio):
-11.567
Reference Allele:
C
-log10(P):
-69.579
MAF:
0.386
Beta (Num):
-0.068
Novel Locus:
Yes ✔️
SE (Num):
0.014
Beta (Den):
0.083
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, Ceramide synthesis.5[1], 6[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism, Ceramide synthesis.5[1], 6[2]

Ratio Explanation:

The ratio reflects the balance between different sphingomyelin species, comparing those with C24 fatty acids to those with C22 or other fatty acids.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Altered ISM1 function likely modulates sphingolipid metabolism, impacting the composition of sphingomyelins.4[1], 7[2] This change in specific sphingomyelin species can affect bile composition and lipoprotein structure, increasing the risk of cholelithiasis and dyslipidemia.6[3], 8[4], 9[5]

Phenotype Driver:

Metabolite-centric[sphingomyelin]

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