There is a long-standing scientific debate as to whether migraine has a primarily neurological or vascular basis45. We analyzed GWAS summary statistics for migraine with aura, migraine without aura, and migraine (all subtypes)16. The migraine (all subtypes) data set contained the data sets for migraine with aura and for migraine without aura, as well as a large number of additional subjects whose subtype was unknown. We found cardiovascular enrichments for migraine without aura with gene expression data, and for migrane without aura and migraine (all subtypes) with EN-TEx data, consistent with previous work16 (Figure 3b). Our analysis of Roadmap data, however, yielded qualitatively different results: the strongest enrichment for migraine (all subtypes) was a neurological enrichment. The top two annotations were neurospheres and fetal brain, neither of which was present in the gene expression data we analyzed nor in EN-TEx. The correlation in enrichments between migraine (all subtypes) and migraine without aura in the gene expression analysis was estimated to be 0.48 (s.e. 0.15), and in the chromatin data was estimated to be 0.60 (s.e. 0.13). Our results are consistent
