# 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 (or medication code) evaluated
chr: chromosome    
rs.id: DBsnp rs identifier
pos: position in the chromosome
ref: reference allele
alt: alternative alelle  
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 effect size
pval: p-value  

Files:

1. Phenotype associations in TMPRSS2 (chromosome 21): 
associations of 72 phenotypes proteins with the genetic variants within the gene and in 100Kb around (985 variants)

<pheno_TMPRSS2.txt>: association results using all available individuals (maximum 36,339). Regression model included sex and age as covariates
<pheno_TMPRSS2_males.txt>: association results using only available males (maximum 15098). Regression model included age as covariate
<pheno_TMPRSS2_females.txt>: association results using only available females (maximum 21241). Regression model included age as covariate

2. Phenotype associations in ACE2 (chromosome X):
associations of 72 phenotypes with the genetic variants within the gene and in 100Kb around (288 variants)

<pheno_ACE2.txt>: association results using all available individuals (maximum 36,339). Regression model included sex and age as covariates
<pheno_ACE2_males.txt>: association results using only available males (maximum 15098). Regression model included age as covariate
<pheno_ACE2_females.txt>: association results using only available females (maximum 21241). Regression model included age as covariate

3. Medication use associations in TMPRSS2 (chromosome 21):
associations of the use of up to 58 medication categories (four-letter code) with the genetic variants within the gene and in 100Kb around (985 variants).~

<med_TMPRSS2.txt>: association results using all available individuals (maximum 36,339). Regression model included sex and age as covariates*
<med_TMPRSS2_males.txt>: association results using only available males (maximum 15098). Regression model included age as covariate*
<med_TMPRSS2_females.txt>: association results using only available females (maximum 21241). Regression model included age as covariate

3. Medication use associations in ACE2 (chromosome X):
associations of the use of up to 58 medication categories (four-letter code)  with the genetic variants within the gene and in 100Kb around (288 variants).~

<med_ACE2.txt>: association results using all available individuals (maximum 36,339). Regression model included sex and age as covariates*
<med_ACE2_males.txt>: association results using only available males (maximum 15098). Regression model included age as covariate*
<med_ACE2_females.txt>: association results using only available females (maximum 21241). Regression model included age as covariate

*Medication code G02B was dropped from this analysis as it is only used by females
~Only variants with minor allele frequency higher than 0.01 were considered in these analyses, because of low sample sizes


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# CHANGELOG
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## 10-04-2020
## creation of this file
