Position Base1 Base2 14 a t 19 a g 25 t c 50 t g 53 g c 60 a t 80 t c 91 t c 93 c g 129 a g 144 a g 148 a c
14 19 25 50 53 60 80 91 93 129 144 148 14 0.2304 0.0784 0.036 -0.0784 0.056 -0.0784 -0.00720000000000001 0.00719999999999998 0.0456 -0.00720000000000001 0.0456 19 0.0784 0.036 -0.0784 0.056 -0.0784 -0.00720000000000001 0.00719999999999998 0.0456 -0.00720000000000001 0.0456 25 0.036 -0.2464 -0.104 -0.2464 0.00879999999999997 -0.00879999999999997 0.0376 0.00879999999999997 0.0376 50 -0.036 0.02 -0.036 -0.028 0.028 -0.036 -0.028 -0.036 53 0.104 0.2464 -0.0088 0.0088 -0.0376 -0.0088 -0.0376 60 0.104 0.012 -0.012 -0.036 0.012 -0.036 80 -0.0088 0.0088 -0.0376 -0.0088 -0.0376 91 -0.2496 -0.0608 0.2496 -0.0608 93 0.0608 -0.2496 0.0608 129 -0.0608 0.2484 144 -0.0608 148
14 19 25 50 53 60 80 91 93 129 144 148 14 0.00 50.00 5.41 1.17 5.41 2.84 5.41 0.05 0.05 1.82 0.05 1.82 19 0.00 0.00 5.41 1.17 5.41 2.84 5.41 0.05 0.05 1.82 0.05 1.82 25 0.00 0.00 0.00 1.10 50.00 9.15 50.00 0.06 0.06 1.15 0.06 1.15 50 0.00 0.00 0.00 0.00 1.10 0.35 1.10 0.65 0.65 1.09 0.65 1.09 53 0.00 0.00 0.00 0.00 0.00 9.15 50.00 0.06 0.06 1.15 0.06 1.15 60 0.00 0.00 0.00 0.00 0.00 0.00 9.15 0.12 0.12 1.09 0.12 1.09 80 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.06 1.15 0.06 1.15 91 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 50.00 2.98 50.00 2.98 93 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.98 50.00 2.98 129 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.98 50.00 144 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.98 148 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
There are only 2 haplotype blocks:
block 1: snps 14, 19, 25, 50, 53, 60, 80
block 2: snps 91, 93, 129, 144, 148
From the Chi-square table, snp 14 is in significant LD with snps 19, 25, 53, and 80. snp 19 is in significant LD with snps 25, 53, 80. snp 25 is in significant LD with snps 53, 60, and 80. ETC. If you draw the snps out linearly on a piece paper and put in the connections between them, you will see that snp 25 is actually in significant LD with snp 60. So there is one long block and not two (most of you pointed out that snps 14-25 are on 1 block while snps 53 to 80 are on another). A common definition of a block is that most snps on that block are in high LD with each other. It doesn't necessarily required EVERY snp to be in LD. We accepted any answer with reasonable criteria for block selection.
A criteria some of you suggested is that one should select a snp that's in greatest LD with others on a block. However, the most important thing one should look at is the NUMBER of other SNPs on a given block a particular SNP is in LD with. So snp 50 is definitely not a good choice for the first block. It doesn't appear to be in LD with any other snps on the block. Snps like this can arise because of recent mutations or population stratification.