Linkage disequilibrium

Linkage disequilibrium for SNPs can be specified in a tab-delimited format similar to PLINK 1.9’s .ld file format. Our format contains only a subset of the full set of columns from PLINK’s:

Name	Type	Description
CHR	string	The name of the chromosome to which this SNP belongs (ex: 1)
BP	integer	The position of this SNP on the chromosome (ex: 10114)
SNP	string	A unique identifier for this SNP in the file (ex: ‘rs1234’)
R	float	Pearson’s correlation coefficient between the variant and some TARGET (ex: 0.42)

Examples

CHR   BP      SNP     R
19    45411941        rs429358        0.999
19    45411947        rs11542041      0.027
19    45411962        rs573658040     -0.012
19    45411965        rs543363163     -0.012
19    45412006        rs563140413     -0.012
19    45412007        rs531939919     -0.012
19    45412040        rs769455        0.006
19    45412079        rs7412  -0.098