# 20250815

#############################
# TWB mQTL summary statistics
#############################

# EAS_TWB:
chr1.gz 
... 
chr22.gz

column 
1    	phe_id phenotype id: CpG ID
2    	phe_chr	The phenotype chromosome
3    	phe_from	Start position of the phenotype (GRCh37)
4    	phe_to	End position of the phenotype (GRCh37)
5    	phe_strd	The phenotype strand
6    	n_var_in_cis	The number variants in the cis window for this phenotype.
7    	dist_phe_var	The distance between the variant and the phenotype start positions.
8    	var_id	The variant ID.
9    	var_chr	The variant chromosome.
10    	var_from	The start position of the variant. (GRCh37)
11    	var_to	The end position of the variant. (GRCh37)
12    	nom_pval	The nominal p-value of the association between the variant and the phenotype.
13    	r_squared	The r squared of the linear regression.
14    	slope	The beta (slope) of the linear regression.
15    	slope_se	The standard error of the beta. Only printed if --std-err is provided.
16    	best_hit	Whether this varint was the best hit for this phenotype.

# Variants information: 
TWB_VCF_info_maf.new.tab.chr1.txt
... 
TWB_VCF_info_maf.new.tab.chr22.txt

CHROM: chromosome (GRCh37)    
POS : position (GRCh37)  
ID  : rs ID    
REF : Non-effect allele    
ALT : Effect allele   
twb_alt_af: Allele frequency of effect allele in Taiwan biobank
snp_id: SNP ID

#############################
# mQTL meta analysis summary statistics
############################

# EAS_meta: 
EAS_meta.chr1_1.TBL.gz
...
EAS_meta.chr22_1.TBL.gz

# EAS_EUR_meta
EAS_EUR_meta.chr1_1.TBL.gz
...
EAS_EUR_meta.chr22_1.TBL.gz


MarkerName: cpgID_snpID e.g: cg24421519_21:35537076:C:T
                             cpgID: cg24421519
                             snpID: 21:35537076:C:T  chr:pos:a1:a2 (GRCh37)
Allele1: Non effect allele
Allele2: Effect allele
Freq1:   Allele frequency of effect allele
Effect:  Effect size of effect allele
StdErr:  Standard error
logPvalue: log10(P-value of meta analysis)
Direction: Direction of effect size 
logHetP:   log10(P-value of heterogeneity test)
TotalSampleSize: Total Sample Size