tricosanoyl sphingomyelin (d18:1/23:0)* to sphingomyelin (d18:0/20:0, d16:0/22:0)*

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

Metabolite Accession: GCST90200123
Name: sphingomyelin (d18:0/20:0, d16:0/22:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs6688818

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Clumped rQTL variant

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SNP Summary

Chr:
1
Beta (Ratio):
0.147
Position:
224326348
SE (Ratio):
0.015
Effect Allele:
C
Z-score (Ratio):
9.807
Reference Allele:
T
-log10(P):
-50.609
MAF:
0.414
Beta (Num):
0.037
Novel Locus:
No
SE (Num):
0.014
Beta (Den):
-0.110
SE (Den):
0.015
No CNV overlap
rQTL cluster:
153
Reaction Distance:
NA
Closest Genes:
FBXO28 DEGS1 NVL AC138393.1 CNIH4

Region: rs680379

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):
-0.342
Position:
12969400
SE (Ratio):
0.015
Effect Allele:
A
Z-score (Ratio):
-22.680
Reference Allele:
G
-log10(P):
-260.550
MAF:
0.384
Beta (Num):
-0.049
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.293
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.6[1], 7[2]

Ratio Explanation:

The ratio reflects the balance between different sphingomyelin species, potentially influenced by SPTLC3's role in creating diverse sphingoid bases during sphingolipid synthesis.1[1], 8[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered SPTLC3 expression likely modifies sphingolipid profiles.1[1], 9[2] Studies suggest a link between sphingolipid metabolism and cholelithiasis, where changes in sphingolipids can affect cholesterol crystallization in bile, contributing to gallstone formation and elevated ALT.10[3], 11[4], 12[5]

Phenotype Driver:

Gene-centric:SPTLC3

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