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Back pain (BP) is a common condition of major social importance and poorly understood pathogenesis. Intervertebral lumbar disc degeneration in all its guises is one of the major biological risk factors for BP. Previously, we identified the locus at 8q24.21 associated with chronic BP, which has been found elsewhere associated with sciatica after surgery for lumbar disc herniation. In the current study we used co-localisation methods to identify the gene most likely to harbor the causal variant. We show that the same functional variant at the 8q24.21 locus is responsible for both lumbar disc degeneration and BP, and we also studied the effects of this locus on related phenotypes. Our results link the locus to intervertebral disc and bone mineral density, but not to anthropometric measurements, thus corroborating the epidemiological evidence. Moreover, the same functional variant at the locus is more likely to affect the expression of the nearby FAM49B gene, rather than the GSDMC gene, which was previously proposed as a causative one for BP.