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

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

Metabolite Accession: GCST90200013
Name: sphingomyelin (d18:1/22:2, d18:2/22:1, d16:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs174560

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
-0.159
Position:
61581764
SE (Ratio):
0.012
Effect Allele:
C
Z-score (Ratio):
-13.621
Reference Allele:
T
-log10(P):
-95.602
MAF:
0.308
Beta (Num):
-0.087
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.072
SE (Den):
0.015
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
FADS1 FADS2 FEN1 TMEM258 MYRF

Region: rs7157785

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
-0.226
Position:
64235556
SE (Ratio):
0.014
Effect Allele:
T
Z-score (Ratio):
-15.721
Reference Allele:
G
-log10(P):
-126.566
MAF:
0.166
Beta (Num):
-0.005
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
0.221
SE (Den):
0.018
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs364585

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.187
Position:
12962718
SE (Ratio):
0.011
Effect Allele:
A
Z-score (Ratio):
-16.870
Reference Allele:
G
-log10(P):
-145.360
MAF:
0.384
Beta (Num):
-0.068
Novel Locus:
No
SE (Num):
0.014
Beta (Den):
0.119
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.3[1], 4[2]

Denominator Metabolite Explanation:

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

Ratio Explanation:

The ratio compares different sphingomyelin species, likely reflecting altered substrate utilization by enzymes like SPTLC3 in de novo sphingolipid synthesis.2[1]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered SPTLC3 activity changes the composition of sphingomyelin species.2[1], 5[2] This shift in the sphingolipid profile is associated with cholelithiasis, potentially by affecting bile composition and promoting gallstone formation.6[3], 7[4], 8[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