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.

Fine-mapping: We used FINEMAP v.1.3.1 and SuSiE v.0.9.1 with GWAS summary statistics and in-sample dosage LD.
Region definition: We defined fine-mapping regions based on a 3 Mb window around each lead variant and merged regions if they overlapped. We excluded the major histocompatibility complex (MHC) region (chr 6: 25–36 Mb) from analysis due to extensive LD structure in the region.
Parameters: We allowed up to 10 causal variants per region and derived up to 10 independent 95% credible sets (CS) and posterior inclusion probabilities (PIP) of each variant using the default uniform prior probability of causality. Other parameters were set to default.
Post-processing: In the manuscript, we reported combined fine-mapping results by taking an average of PIP of the two methods, while excluding variants with a substantial PIP difference (> 5%) to further improve fine-mapping accuracy. If either fine-mapping method failed (e.g., due to conversion failure or available memory restrictions), we used successful results from the other method. If both of the methods failed, we excluded these regions from analysis.

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:

Kanai, M., et al. Insights from complex trait fine-mapping across diverse populations. medRxiv 2021.
Sakaue, S. & Kanai, M., et al. A cross-population atlas of genetic associations for 220 human phenotypes. Nat. Genet. 2021.

Contact

Masahiro Kanai (mkanai@broadinstitute.org)