Transcriptome–neuroimaging spatial correlation analyses demonstrated that the 479 gene levels of expression (top five positively correlated genes: MTMR2, EPN3, EIF5A2, RCAN2, RAMP3; top five negatively correlated genes: RIIAD1, PLPPR4, LYRM9, PGM2L1, GABRA5) were significantly associated with GMV changes, and 1547 gene expression measures were significantly related to ALFF alterations in OSA (top five positively correlated genes: PLPPR4, FAM171B, UCHL3, TMEM158, APOC1; top five negatively correlated genes: LOC100506388, NFIC, DOK3, SYT2, ADAM23). Here, RCAN2 is linked to obstructive sleep apnea syndrome.