Fine-mapping results of 79 complex traits in BBJ

This release (hum0197.v5) contains fine-mapping results of 79 complex traits in BBJ as described in Kanai, M., et al. (2021). In addition, we release GWAS summary statistics of additional 11 phenotypes that are not reported in the previous release (hum0197.v3). GWAS summary statistics for the remaining 68 phenotypes are available in hum0197.v3.

For GWAS summary statistics, please refer to the dictionary file of hum0197.v3 and Sakaue, S. & Kanai, M., et al. (2021) for more details.

UKBB fine-mapping results described in Kanai, M., et al. (2021) are available at the Finucane Lab website. FinnGen fine-mapping results are available at the FinnGen website.

Methods:

Please refer to Kanai, M., et al. (2021) for more details.

Uploaded files

File name Descriptions
BBJ.{TRAITNAME}.Kanai2021.FINEMAP.tsv.gz Fine-mapping result from FINEMAP
BBJ.{TRAITNAME}.Kanai2021.SuSiE.tsv.gz Fine-mapping result from SuSiE

Column descriptions

FINEMAP

# column name Descriptions
1 chromosome chromosome
2 position position (hg19)
3 allele1 reference allele (hg19)
4 allele2 alternative allele (hg19). This allele is the effect allele.
5 variant variant ID (chromosome:position:ref:alt)
6 rsid rsID (if available) or the same variant ID
7 af_allele2 allele frequency of allele2 (alt)
8 beta_marginal marginal effect size of allele2
9 se_marginal standard error of beta_marginal
10 pvalue p value of association for beta_marginal
11 region fine-mapping region (chromosome:start-end)
12 pip posterior inclusion probability (PIP)
13 cs_id 95% credible set (CS) ID. This is a unique ID per each region and becomes -1 if a variant does not belong to any CS.
14 beta_posterior Posterior mean effect size of allele2
15 sd_posterior standard deviation of beta_posterior

SuSiE

# column name Descriptions
1 chromosome chromosome
2 position position (hg19)
3 allele1 reference allele (hg19)
4 allele2 alternative allele (hg19). This allele is the effect allele.
5 variant variant ID (chromosome:position:ref:alt)
6 rsid rsID (if available) or the same variant ID
7 af_allele2 allele frequency of allele2 (alt)
8 beta_marginal marginal effect size of allele2
9 se_marginal standard error of beta_marginal
10 pvalue p value of association for beta_marginal
11 region fine-mapping region (chromosome:start-end)
12 pip posterior inclusion probability (PIP)
13 cs_id 95% credible set (CS) ID. This is a unique ID per each region and becomes -1 if a variant does not belong to any CS.
14 beta_posterior Posterior mean effect size of allele2
15 sd_posterior standard deviation of beta_posterior
16-25 alpha{1..10} posterior inclusion probabilities for the n-th single effect
26-35 lbf_variable{1..10} log Bayes factors for the n-th single effect

Reference

If you use this dataset, please cite the following papers:

Contact

Masahiro Kanai (mkanai@broadinstitute.org)