How to convert your Affymetrix SNP data into Haploview format by SNP tools
The basic steps are identical to those converting own few SNPs to Haploview. The difference is that the Affymetrix chip data is so big that SNPs are listed in rows and samples in columns.
Select the data range from the cell of "SNP ID", remember to set the SNP type to "A,B,AB,NoCall":