I am quite new to the field of GWAS (genome-wide association studies), and I'm combining GWAS results and single cell analysis on type-1 diabetes (T1D), to see the role of cell specificity on the disease.
However, I don't understand one aspect about GWAS results. The GWAS results lists all the significant SNPs (low p-value) from a certain study on a particular disease. After that, those SNPs are mapped to genes using either positional mapping (using windows), eQTL mapping, or even both.
However, some SNPs do not map to any genes using both positional and eQTL mapping procedure. Some removed SNPs even have a lower p-value than those which are mapped to genes.
Here is my question: since all the listed SNPs are supposed to be significant (tiny p-value), how can those SNPs which are highly correlated to the disease also show no association towards any gene. How do these SNPs give rise to the disease?
I would like to thank you in advance. Sorry if I'm using wrong jargon or anything, and please let me know, if you want any further clarification.