glycodeoxycholate 3-sulfate to glycochenodeoxycholate glucuronide (1)

Numerator Metabolite

Metabolite Accession: GCST90200026
Name: glycodeoxycholate 3-sulfate
Hmdb Id: HMDB0341325
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Structure of glycochenodeoxycholate glucuronide (1)
Metabolite Accession: GCST90200693
Name: glycochenodeoxycholate glucuronide (1)
Hmdb Id: HMDB0002579
Super Pathway: NA
Sub Pathway: NA
Inchikey: ABFZMYIIUREPLL

Associated Genomic Regions

Region: rs55971546

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Clumped rQTL variant

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SNP Summary

Chr:
13
Beta (Ratio):
0.394
Position:
103718308
SE (Ratio):
0.031
Effect Allele:
T
Z-score (Ratio):
12.667
Reference Allele:
C
-log10(P):
-82.992
MAF:
0.047
Beta (Num):
0.385
Novel Locus:
No
SE (Num):
0.037
Beta (Den):
-0.009
SE (Den):
0.036
No CNV overlap
rQTL cluster:
225
Reaction Distance:
NA
Closest Genes:
SLC10A2 ERCC5 BIVM-ERCC5 BIVM KDELC1

Region: rs62129966

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
-0.252
Position:
48374950
SE (Ratio):
0.018
Effect Allele:
A
Z-score (Ratio):
-14.090
Reference Allele:
C
-log10(P):
-102.142
MAF:
0.160
Beta (Num):
-0.250
Novel Locus:
No
SE (Num):
0.021
Beta (Den):
0.002
SE (Den):
0.021
No CNV overlap
rQTL cluster:
7
Reaction Distance:
NA
Closest Genes:
SULT2A1 TPRX2P CRX TPRX1 SEPW1

LLM Analysis

Numerator Metabolite Explanation:

Bile acid biosynthesis

Denominator Metabolite Explanation:

Bile acid metabolism

Ratio Explanation:

The ratio reflects altered bile acid detoxification, where decreased SULT2A1 function may favor glucuronidation over sulfation, impacting bile composition and increasing cholelithiasis risk.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Reduced SULT2A1 activity, indicated by pQTL data, alters bile acid metabolism. This shift, reflected in the glycodeoxycholate 3-sulfate to glycochenodeoxycholate glucuronide ratio, contributes to the formation of gallstones (cholelithiasis), a phenotype also linked to SLC10A2 variants that affect bile acid reabsorption.1[1], 3[2], 4[3], 5[4]

Phenotype Driver:

Gene-centric:SULT2A1

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