Colocalization

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Colocalization

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What is fine-mapping of GWAS loci?

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An estimation of the probability that a variant is not causal.

Separation of the variants based on LD contamination.

An estimation of the probability that a variant is causal.

The probability that the signal at the region is due to the same causal variant for both the expression and complex traits.

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What does PIP stand for?

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Posterior Inclusion Probability

Posterior Interior Probability

Personal Identity Probability

Probability of Information Priority

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What is the interpretation PIP?

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The probability a variant is LD contaminated.

The posterior probability a variant is not causal.

The probability of the variant expressing a separate phenotype due to random chance.

The posterior probability that a variant is causal.

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How are p-values and PIP related to each other?

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How do colocalization methods work?

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Colocalization tries to estimate the probability that the causal variants of the expression trait is the same as the causal variant of the complex trait.

Colocalization tries to estimate the probability that the causal variants of the expression trait is dependent on all the variants of the complex trait.

Colocalization tries to estimate the probability that all the variants of the expression trait are dependent on all the variants of the complex trait.

Colocalization tries to estimate the probability that the causal variants of the expression trait is dependent on the causal variant of the complex trait.

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How many SNPs are used for finemapping the gwas?

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3853

2111

5628

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How many SNPs are used for finemapping the eQTLs?

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2111

5628

3853

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How many SNPs were used to run coloc? Hint: overlap between gwas and eqtl SNPs

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What is the alignment of "ff". Hint: use check_alignment()

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What are the results of summary(S4)

Copy the output of "print(susie.res$summary)"

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