# README
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# GENERAL INFO
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URL:https://molgenis21.gcc.rug.nl/menu/main/home
Study title:Lack of genetic association with human phenotypes at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection 
Created by: Esteban Lopera, Adriaan van der Graaf, Serena Sanna
Created on: 04/2020

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DATA DESCRIPTION
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Columns:

feat: phenotype that was evaluated
chr: chromosome (X chromosome is coded as `23`)
rs.id: DBsnp rs identifier
pos: position in the chromosome
ref: reference allele
alt: alternative allele (also the effect allele)
AF.alt: Allele frequency of alternative allele in the evaluated model
AC.alt: Allele count  of alternative allele in the evaluated model
num: Total number of individuals included in the model
beta: coefficient of the genetic variant in the model (effect size)
SE: standard deviation of the beta 
pval: p-value  
analysis: subset of the analysis that was done (`joint` is males and females analyzed together, `males` is only males and `females` only includes females in the analysis)
ERRCODE: Errorcode if there are no association results from plink2 v2.00a3LM
covariates: covariates used in this model. (`none` indicates no covariates used, `age_and_sex` includes age and sex as a covariate and `age` only includes age as a covariate)


File:

1. Phenotype associations ACE2 and TMPRSS2: 
Associations of 104 circulating proteins with the genetic variants whithin the TMPRSS2 or ACE2 gene and in 100Kb around them.
Each variant-gene combination has been tested 6 times: 3 sex specific analyses and 2 covariate specific analyses.
The sex specific analyses, analyzed all sexes jointly (analysis column: `joint`), or each sex separately (analysis column: `males` or `females`). 
The covariate specific analysis either analyzed with or without covariates: `sex_and_age` when analysis = `joint` and `age` otherwise. 
`none` is reported when no covariates were analyzed.
We included the `none` analysis due to colinearity issues between the variant and the covariates. Making it sometimes difficult to discern the effect of the variant and the effect of the covariate

 
<2020_04_14_all_snps_all_cytokine_pheno_v3.txt>





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# CHANGELOG
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## 14-04-2020
## creation of this file
