Despite the unique qualities of the cells, chimerism does not always produce noticeable effects. Some physical changes are too subtle to suggest any underlying cause, much less differing genetics. For example, a person may have one straight and one hitchhiker's thumb or have slightly different hair growth rates on different areas of the body. Chimerism is also one of the causes of heterochromia, or eyes of different colors. If the fused cells were zygotes of different sexes, the resulting individual may have ambiguous or intersex genitalia. If the fused cells were blastocysts of different sexes, it is possible for genitals of both sexes to form, either ovary and testis, or ovotestes.

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