decodemehit

Another locus that was just below the significance threshold (p = 5.4 × 10⁻⁷) in DecodeME but unfortunately, it's hard to determine which gene it points to. There are lots of genes in this region and the credible set is very spread out. Many of the SNPs are inside SNTA1 and CBFA2T2 so they are...

Another DecodeME hit that remained just below the significance threshold (p = 2.9 × 10⁻⁷). The T risk allele was present in 81.9% of cases and 79.3% in controls, resulting in an odds ratio of 1.086 per copy of T. The 95% credible set using SUSIE consists of 22 SNPs that lie in the RNA...

This locus was just below the significance threshold in DecodeME. The credible set includes 189 SNPs and all lie in LRRC7, which is the most likely causal gene. The eQTL showed that LRRC7 colocalized with several different tissues but with PP.H4 around 0.6-0.8, so it wasn't a perfect match...

Perhaps not the most interesting locus but it does have a signal just below the significance threshold (p = 1.9 × 10⁻⁷) in DecodeME. The credible set lies in the gene ZNF644 which is also the most likely candidate. In the Hi-C on the 3D-folding BARHL was in the same domain and had multiple...

This is one of the signals in DecodeME that was just below the significance threshold (top hit p = 2.43e-7). It lies in a dense region with lots of genes. The credible set lies above CCDC92 and ZNF664 and to a lesser extent DNAH10.

The lead variant at this locus is 15:54866724:A:G (rs7165327) with a p-value of 7.62E-09. DecodeME labelled CCPG1 as a Tier 2 gene. The nearest protein coding genes are UNC13C (at 234,980 bp), and then RSL24D1 (at 314,073 bp). Though rs7165327 was a significant DecodeME hit, none of the nearest...

The 15th most significant locus in DecodeME is overlapping the gene DCC. The lead variant at this locus is 18:53232948:C:T (rs72923287) with a p-value of 2.48x10-7. GeneCards summary for DCC: Full gene name: DCC Netrin 1 Receptor "DCC" stands for "Deleted In Colorectal Carcinoma" The...

From a discussion on the Eccentric Medium Spiny Neurons thread: DecodeME identified HTT as of interest.

The locus near SHISA6 wasn't quite genome-wide significant, but it was close at p=8.26e-08. From GeneCards: Here is a plot of this locus (LocusZoom link): Edit: The lead variant at this locus is: 17:11,325,637:G:C / rs1546559

I didn’t see a thread about SOX6, apologies if I missed it SOX6 seems interesting as it is not only a peak in LocusZoom itself but also a Transcription Factor Binding Site mentioned in Genehancer data for promoters and enhancers for many (well most) other genes in the DecodeME candidate gene...

A quick look on AI. The NEGR1 (Neuronal Growth Regulator 1) gene, located on chromosome 1p31.1, encodes a GPI-anchored cell adhesion molecule critical for brain development, synaptic organization, and neuronal connectivity. Strongly associated with obesity, depression, and neurodevelopmental...

These are the main candidate genes suggested by the data from the DecodeME study based on different methods: Tier 1 and 2 genes as defined by the DecodeME paper, significant genes using MAGMA test, and the nearest genes to the top 25 most significant loci. I posted the same information on the...

One of the candidate genes in the DecodeME preprint. Curcumin increases PRDX6 expression.

DecodeME candidate ME gene From the Candidate Genes document CHROMOSOME 6p Chr6p contained seven Tier 1 genes. ******************** HFE (Tier 1) • Protein: Homeostatic iron regulator protein. UniProt. GeneCards. The allele that increases the risk of ME/CFS is associated with increasing HFE...

DecodeME candidate ME gene From the Candidate Genes document CHROMOSOME 20 Chr20 contained seven Tier 1 genes. *************** CSE1L (Tier 1) • Protein: Chromosome segregation 1-like (also known as exportin-2). UniProt. GeneCards. The allele that increases the risk of ME/CFS is associated...

DecodeME candidate ME gene From the Candidate Genes document CHROMOSOME 17 Chr17 contained one Tier 1 gene. **************** CA10 (Tier 1) • Protein: Carbonic anhydrase-related protein 10. UniProt. GeneCards. Note that this gene encodes a protein that lacks catalytic activity. The allele...

DecodeMe Candidate Gene CHROMOSOME 15 Chr15 contained no Tier 1 genes and one Tier 2 gene. ********************* CCPG1 (Tier 2) • Protein: Cell cycle progression 1. UniProt. GeneCards. • Molecular function: Involved in positive regulation of cell cycle and positive regulation of cell...

DecodeMe Candidate Gene CHROMOSOME 13 Chr13 contained no Tier 1 genes and one Tier 2 gene. ******************** OLFM4 (Tier 2) • Protein: Olfactomedin-4. UniProt. GeneCards. • Molecular function: OLFM4 facilitates cell adhesion, most probably through interaction with cell surface lectins...

CHROMOSOME 12 (GWAS-2) Chr12 contained three Tier 1 genes. Image of the 2025 DecodeME results by @ME/CFS Science Blog: ******************** SUDS3 (Tier 1) • Protein: SIN3A corepressor complex component, also known as SDS3. UniProt. GeneCards. The allele that increases the risk of ME/CFS is...

DecodeME candidate ME/CFS gene ******************** FBXL4 (Tier 2) • Protein: F-box/LRR-repeat protein 4. UniProt. GeneCards. • Molecular function: Component of the mitochondria-localised SCF-FBXL4 ubiquitin E3 ligase complex. This complex restricts mitophagy by controlling the degradation...