Simply put, my question is: I have a SNP from a GWAS that if I find records associated with it in UCSC snp135, I get 2 records, one on chr17 and one on chr17ctg5hap1, what should I do?
Since it's in that region (which I assume to be a region with strong LD), there are also a bunch of other significant SNPs near-by. Is this interesting or does it present an opportunity for further analysis?
For example, I was thinking maybe certain haplotypes are more likely to be disease-prone? Worth looking into? How?