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I'm looking for publicly available genotype data (eg. 1000 Genomes or HapMap) that also has associated phenotypes (any traits). I'm wanting to use it as a test run for a GWAS pipeline. Does anyone know if this exists anywhere?

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See openSNP here:

https://opensnp.org/

It is a web site for people to upload their own genetic datasets, providing freely-accessible public data with annotated phenotypes.

openSNP allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results by getting the latest primary literature on their variations, and help scientists find new associations.

The large collaborative research genetic data projects typically have very strict access constraints due to the realisation that genetic data is personally-identifiable data, and the expectation of anonymity. That means there's a low likelihood that a large research project will make their phenotype + genotype data publicly available.

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