Chunk #47 — Other Considerations for the Social Scientist — Analyzing genetic data

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Incorporating genetics into your studies: a guide for social scientists.

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is to say, if you are testing a group of highly correlated SNPs, you would expect a similar association pattern across them. In contrast, if SNPs are located in different LD blocks (i.e., have a low correlation), it would not be concerning if they yielded different association results.