tricosanoyl sphingomyelin (d18:1/23:0)* to sphingomyelin (d18:1/14:0, d16:1/16:0)*

Numerator Metabolite

Structure of tricosanoyl sphingomyelin (d18:1/23:0)*
Metabolite Accession: GCST90200034
Name: tricosanoyl sphingomyelin (d18:1/23:0)*
Hmdb Id: HMDB0012105
Super Pathway: NA
Sub Pathway: NA
Inchikey: SXZWBNWTCVLZJN

Denominator Metabolite

Structure of sphingomyelin (d18:1/14:0, d16:1/16:0)*
Metabolite Accession: GCST90199945
Name: sphingomyelin (d18:1/14:0, d16:1/16:0)*
Hmdb Id: HMDB0012097
Super Pathway: NA
Sub Pathway: NA
Inchikey: KYICBZWZQPCUMO

Associated Genomic Regions

Region: rs8008068

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
-0.401
Position:
64233717
SE (Ratio):
0.017
Effect Allele:
G
Z-score (Ratio):
-23.495
Reference Allele:
A
-log10(P):
-279.396
MAF:
0.166
Beta (Num):
0.022
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
0.423
SE (Den):
0.019
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs4814175

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):
-0.166
Position:
12959094
SE (Ratio):
0.013
Effect Allele:
A
Z-score (Ratio):
-12.459
Reference Allele:
T
-log10(P):
-80.365
MAF:
0.386
Beta (Num):
-0.048
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.118
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.4[1], 5[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2]

Ratio Explanation:

The ratio reflects the balance between very-long-chain (C23:0) and shorter-chain sphingomyelins.6[1], 7[2] SGPP1's influence on precursor pools may alter this balance.2[3], 3[4]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variation in SGPP1 likely alters sphingolipid metabolism, reflected in the ratio of very-long-chain to shorter-chain sphingomyelins.1[1], 6[2] This compositional change in key lipoprotein and membrane lipids contributes to dyslipidemia and an increased risk of cholelithiasis.8[3], 9[4], 10[5]

Phenotype Driver:

Metabolite-centric[both]

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