The study found that one variant increased the risk of oestrogen receptor positive disease by 14 per cent, while a second raised the chance by 11 per cent.
Researchers said the finding provided important clues about the way disease is caused, implicating a gene called KLF4, which is thought to help control the way cells grow and divide.
The research involved scientists from more than 130 institutions worldwide, including the London School of Hygiene and Tropical Medicine, and the University of Cambridge.
Researchers were looking for one-letter differences in DNA code that were more likely to be found in women with breast cancer than those without the disease, using a state-of-the-art genetic technique called fine mapping.
Study leader Dr Nick Orr said: "Our study zoomed in on an area of our genome that we knew was linked to breast cancer risk, and has identified two new genetic variants that add significantly to our knowledge about the genetic causes of the disease.
"The variants we identified are specifically associated with the most common, oestrogen receptor positive, form of breast cancer.
"The more genetic risk factors for breast cancer we discover, of which there are currently more than 80, the more accurately we will be able predict who is at risk of getting the disease. Ultimately this will be vital for designing preventative strategies against breast cancer."
Dr Emma Smith, senior science information officer at Cancer Research UK, praised the results.
She said: "Thanks to modern technology we're building an increasingly detailed picture of the small variations in DNA that can influence a woman's risk of breast cancer.
"The next challenges are understanding the biology underpinning their effects, so we can use this information to predict individual risk more accurately, improve screening and find better ways to treat and prevent breast cancer."
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Study finds genetic mutation behind most common breast cancer