Fifth, we added additional data types to attempt to improve understanding of individual loci. For the intergenic associations, we evaluated total-stranded RNA-seq data from human brain and found no evidence for unannotated transcripts in these regions. A particularly important data type is assessment of DNA-DNA interactions which can localize a GWA finding to a specific gene that may be nearby or hundreds of kb away52–54. We integrated the major depression results with “easy Hi-C” data from brain cortical samples (3 adult, 3 fetal, > 1 billion reads each). These data clarified three associations. The statistically independent associations in NEGR1 (rs1432639, P=4.6×10−15) and over 200 kb away (rs12129573, P=4.0×10−12) both implicate NEGR1 (Supplementary Fig. 3a), the former likely due to the presence of a reportedly functional copy number polymorphism (see Supplementary Note) and the presence of intergenic loops. The latter association has evidence of DNA looping interactions with NEGR1. The association in SOX5 (rs4074723) and the two statistically independent associations in RBFOX1 (rs8063603 and rs7198928, P=6.9×10−9 and 1.0×10−8) had only intragenic associations, suggesting that the genetic variation in the regions of
