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A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252
BRCA1
mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (
P
=9.2 × 10
−20
), ER-negative BC (
P
=1.1 × 10
−13
),
BRCA1
-associated BC (
P
=7.7 × 10
−16
) and triple negative BC (
P
-diff=2 × 10
−5
). Genotype-gene expression associations are identified for candidate target genes
ANKLE1
(
P
=2 × 10
−3
) and
ABHD8
(
P
<2 × 10
−3
). Chromosome conformation capture identifies interactions between four candidate SNPs and
ABHD8
, and luciferase assays indicate six risk alleles increased transactivation of the
ADHD8
promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces
ANKLE1
downregulation; and mRNA stability assays indicate functional effects for an
ANKLE1
3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate
ABHD8
and perhaps
ANKLE1
expression, and indicate common mechanisms underlying breast and ovarian cancer risk.
A region on chromosome 19p13 is associated with the risk of developing ovarian and breast cancer. Here, the authors genotyped SNPs in this region in thousands of breast and ovarian cancer patients and identified SNPs associated with three genes, which were analysed with functional studies.