The SNP-eQTL analyses were performed across diverse tissues examining the correlation between marker alleles and transcript levels at the associated BMD loci. Fourteen of the BMD-associated SNPs correlated with the expression of one or more of the nearby genes with P < 5×10−5 and were either the strongest cis-variants, or good surrogates thereof, for those genes (Supplementary Tables 14 and 15). The most significant BMD-SNP eQTL was observed for rs10835187[T] with reduced expression of the LIN7C gene at the 11p14.1 locus (P = 2.8×10−39 in adipose tissue). Of particular interest were BMD-SNP cis-variants at three loci that were also associated with fracture including: 1p36.12, 4q22.1 and 17q21.31. At 1p36.12, rs6426749[G] correlated with reducedWNT4 expression in fibroblast, osteoblast and adipose tissue; at 4q22.1 rs6532023[G] correlated with reduced SPP1 (osteopontin) expression in adipose tissue and at 17q21.31 rs227584[A] correlated with increased C17orf65 expression in monocytes, adipose tissue, whole blood and lymphoblasts.
