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Open GWAS has another tool called the Genotype-Phenotype Map where it can do actual colocalization testing against many GWAS datasets using uploaded summary stats. I uploaded the DecodeME GWAS-1 summary stats. The results are on the following page, indicating which traits colocalize (share a...

I used the Open GWAS API to retrieve traits associated with the lead variants at each of the 8 DecodeME loci. I wrote more details on the CA10 locus thread. Keep in mind that multiple traits being significant for the same variant doesn't necessarily mean the same variant is causal for all of...

I used the Open GWAS API to retrieve traits associated with the lead variants at each of the 8 DecodeME loci. I wrote more details on the CA10 locus thread. Keep in mind that multiple traits being significant for the same variant doesn't necessarily mean the same variant is causal for all of...

I used the Open GWAS API to retrieve traits associated with the lead variants at each of the 8 DecodeME loci. I wrote more details on the CA10 locus thread. Keep in mind that multiple traits being significant for the same variant doesn't necessarily mean the same variant is causal for all of...

I used the Open GWAS API to retrieve traits associated with the lead variants at each of the 8 DecodeME loci. I wrote more details on the CA10 locus thread. Keep in mind that multiple traits being significant for the same variant doesn't necessarily mean the same variant is causal for all of...

Yes good point. We can at least see the total sample size for studies in the table above, and they're all around 350,000 to 450,000 for this group of datasets. Though unbalanced group sizes in binary traits, for example, could make a study's effective sample size smaller, making the findings...

There was an association between people getting more infections and their relatives developing tic disorders, even when they controlled for relatives' infections, so they say this more likely represents common genetic causes for both getting infections and developing tic disorders, rather than...

Proneness to infections and familial risk of tic disorders Background Postinfectious autoimmune processes are hypothesized to be causally implicated in tic disorders, including Tourette syndrome and chronic tic disorder. However, this hypothesis remains controversial. In this nationwide...

I assume you're referring to this section: Here are those genes from Supplementary Table 9:

Yes. In Table 3 of the DecodeME paper, the variant is 1:173846152:T:C. Since C is the letter at the end, that's what the odds ratio in the table is describing. The odds ratio is less than 1 (0.927), so having a C is associated with decreased risk. Thus, having a T is associated with increased...

I used the Open GWAS API to retrieve traits associated with the lead variants at each of the 8 DecodeME loci. I wrote more details on the CA10 locus thread. Keep in mind that multiple traits being significant for the same variant doesn't necessarily mean the same variant is causal for all of...

I used the Open GWAS API to retrieve traits associated with the lead variants at each of the 8 DecodeME loci. I wrote more details on the CA10 locus thread. Here are traits associated with rs12071663/1:173846152:T:C (the lead DecodeME variant near RABGAP1L), with p<1e-6, starting from most...

For the PheWAS analysis I did a few posts ago (looking up which other traits have significant associations at a variant), I used GWAS Atlas. They have 4,756 GWAS datasets, and they have not added any datasets since 2019. I found out that IEU Open GWAS also has PheWAS functionality, and they...

Yes, this is showing linkage disequilibrium. The following plot actually shows the strength of LD between each of the variants in the plot with the lead variant (purple diamond). The variants in red have very strong LD with the lead variant, so would be expected to show up very often in people...

Postorgasmic illness syndrome: a clinical case series of 11 patients Gokani, Nikunj S; Jacob, Niva; Deshpande, Sandip M Extract Postorgasmic illness syndrome (POIS) is an uncommon clinical condition that remains poorly defined since its initial description by Waldinger and colleagues in 2002.1...

Both sexes show hypomethylation at PTPRN2: Hypomethylation group has longer illness (17 ± 2 years vs. 11 ± 2 years) Fig 2a,b: That's a large difference. I wonder what the gap between high and low values in the HC group represents.

I sometimes search for nutrition reviews to see what the state of the science is. The field seems very hard to conclusively determine anything from, as RCTs are very difficult in nutrition, so confounding is a huge issue, and lots of the research is done using questionnaires, which is open to...

Interesting commentary about the field of chemical exposomics: Will Chemical Exposomics Be Ready for a Human Exposome Project? Martin, Jonathan W. Web | DOI | PDF | Environmental Science & Technology | Open Access | 2026 Snippets:

It's using an older assembly/coordinate system called GRCh37. The more recent one that DecodeME uses is called GRCh38. Defining where exactly a SNP is on a chromosome isn't an exact science, so as they learn more, they make updates to the positions. "Liftover" is converting the coordinates to a...

Here are the top 20 most significant traits associated with the lead DecodeME SNP at the CA10 locus (rs34626694) on GWAS Atlas. Reaction time is also fairly significant.