1% is a lot for a complex trait like depression. All genetics combined predicted/determines ~37%, and the part specifically attributable to SNPs is ~32% (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404250/). So that one variant is explaining more like 3% of the genetics; another 32 such variants and about all the possible genetics is known! And they could potentially lead to major insights by looking at what the Neanderthal variant does differently from the regular Homo sapiens variant does; a recent example of this was synaptic pruning & schizophrenia.