The fine-mapped associations of 35 lab biomarkers described in 'Genetics of 35 blood and urine biomarkers in the UK Biobank'

The dataset contains the output from FINEMAP, a software to identify causal variants from genome-wide association summary statistics, for 35 biomarker traits described in the following preprint:<br>N. Sinnott-Armstrong*, Y. Tanigawa*, et al, Genetics of 38 blood and urine biomarkers in the UK Biobank. bioRxiv, 660506 (2019). doi:10.1101/660506<br><br>Note that we are preparing a revised version of the manuscript and this dataset contains 35 (instead of 38) biomarker phenotypes.<br><br>For each trait, we provide a tar archive file which contains the full output from FINEMAP for the regions with at least one genome-wide significant associations (p &lt; 5e-9) from the multi-ethnic GWAS meta-analysis within UK Biobank. The content of the tar archive is organized by directories, named as <code>chr[CHROM]/[TRAIT]/range[RANGE]</code>, and contains the following files: <code>GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].bdose.zst</code><code>GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].config.zst</code><code>GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].cred.zst</code><code>GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].ld.zst</code><code>GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].master.zst</code><code>GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].snp.zst</code><code>GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].z.zst</code> where, [TRAIT]<code></code><code></code>: trait name[CHROM]<code></code><code></code>: chromosome[RANGE]<code></code><code></code>: the range of the region in the format of <code>[start position]-[end position]</code>. We provide the list of traits and regions included in this data release in <code>FINEMAP.index.tsv</code>. This is a flat table with 3 columns: trait: the biomarker traitchr: chromosomerange: the range Note that we used GRCh37/hg19 genome reference in the analysis and the BETA is always reported for the alternate allele. Please check the FINEMAP paper and software documentation for the detailed explanation of the file formats. Benner, C. et al. FINEMAP: efficient variable selection using summary data from genome-wide association studies. Bioinformatics 32, 1493–1501 (2016).Christian Benner. FINEMAP. http://christianbenner.com/. Also, all the files in the tar archive is compressed with Zstandard (as indicated by the <code>.zst</code> extension). You can check the contents with <code>zstdcat</code> command and uncompress the files with <code>zstd -d [file.zst]</code>. The Zstandard software can be built from source, or simply available from conda (https://anaconda.org/conda-forge/zstd), pip (https://pypi.org/project/zstd/) or brew (https://formulae.brew.sh/formula/zstd). Please check Zstandard website (http://facebook.github.io/zstd/) for more information.

本数据集包含FINEMAP（一款从全基因组关联研究汇总统计量中识别因果变异的软件）的输出结果，对应35种生物标志物性状，相关内容见于下述预印本：N. Sinnott-Armstrong*、Y. Tanigawa*等人的《英国生物库（UK Biobank）中38种血液与尿液生物标志物的遗传学研究》，发表于bioRxiv, 660506 (2019). doi:10.1101/660506

请注意，我们正在修订该手稿的正式版本，本数据集实际包含35种（而非预印本中提及的38种）生物标志物表型。

针对每一种性状，我们提供了一个tar归档文件，其中包含英国生物库内多族群全基因组关联研究（GWAS）荟萃分析中至少存在1个全基因组显著性关联（p < 5e-9）的区域的完整FINEMAP输出结果。该tar归档文件的内容以目录形式组织，目录命名格式为`chr[CHROM]/[TRAIT]/range[RANGE]`，其中包含以下文件：
`GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].bdose.zst`
`GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].config.zst`
`GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].cred.zst`
`GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].ld.zst`
`GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].master.zst`
`GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].snp.zst`
`GLOBAL_[TRAIT]_chr[CHROM]_range[RANGE].z.zst`
其中，[TRAIT]为性状名称，[CHROM]为染色体编号，[RANGE]为区域范围，格式为`[起始位置]-[终止位置]`。我们在`FINEMAP.index.tsv`文件中提供了本次数据发布包含的所有性状与区域列表。该文件为三列平面表格，列名分别为：trait（生物标志物性状）、chr（染色体）、range（区域范围）。

请注意，本分析采用GRCh37/hg19基因组参考序列，且所有报告的BETA值均针对替代等位基因。如需了解文件格式的详细说明，请参阅FINEMAP相关论文与软件文档：Benner, C. et al. FINEMAP: efficient variable selection using summary data from genome-wide association studies. Bioinformatics 32, 1493–1501 (2016). Christian Benner. FINEMAP. http://christianbenner.com/。此外，tar归档中的所有文件均采用Zstandard压缩（文件扩展名`.zst`即为标识）。你可以使用`zstdcat`命令查看文件内容，或使用`zstd -d [file.zst]`命令解压文件。Zstandard软件可从源码编译获取，也可通过conda（https://anaconda.org/conda-forge/zstd）、pip（https://pypi.org/project/zstd/）或Homebrew（https://formulae.brew.sh/formula/zstd）快速安装。如需更多信息，请访问Zstandard官方网站（http://facebook.github.io/zstd/）。