LDSPEC_data_release_120223

Data release accompanying initial submission (120223) of the paper "Pervasive correlations between causal disease<br>effects of proximal SNPs vary with functional annotations and implicate stabilizing selection".snp_info.zip: .pvar file of 14,820,648 imputed SNPs. "snp_list_chr@.MAF_001_INFO_06.txt" contains the list of MAF&gt;0.1% and INFO&gt;0.6 SNPs. "ukb_imp_chr@_v3_aa.pvar" contains the final set of SNPs where "REF_Chimp" was used as the ancestral allele (opposite of derived allele)annot_single165.zip: 165 single-SNP annotations in the baseline-SP model (across 14,820,648 imputed SNPs).annot_pair136.zip: 136 SNP-pair annotations in the baseline-SP model (across 14,820,648 imputed SNPs).main.avgr: LDSPEC ".avgr" file for average LD (r) of the SNP-pair annotations.trait_list_paper.txt: list of 70 diseases/traits analyzed in the paper.ldspec_results.zip: LDSPEC results for 70 diseases/traitsAdditionally, other data files are in separate folders:LD scores and directional LD scores: https://figshare.com/account/projects/188052/articles/24716901GWAS summary statistics: https://figshare.com/account/projects/188052/articles/24716952 <br><br>

本数据集配套于论文《近端单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的因果疾病效应间的普遍相关性随功能注释变化并暗示稳定选择》的2023年12月2日首次投稿版本。

各数据文件详情如下：
1. snp_info.zip：包含14,820,648个插补SNP的.pvar格式文件。其中"snp_list_chr@.MAF_001_INFO_06.txt"收录了最小等位基因频率（Minor Allele Frequency, MAF）>0.1%且填充信息评分（INFO）>0.6的SNP列表；"ukb_imp_chr@_v3_aa.pvar"则收录了以黑猩猩参考等位基因作为祖先等位基因（与衍生等位基因相对）的最终SNP集合。
2. annot_single165.zip：包含基线-SP（baseline-SP）模型中针对14,820,648个插补SNP的165个单SNP功能注释。
3. annot_pair136.zip：包含基线-SP（baseline-SP）模型中针对14,820,648个插补SNP的136个SNP对功能注释。
4. main.avgr：用于计算SNP对功能注释平均连锁不平衡（Linkage Disequilibrium, LD）r值的LDSPEC格式.avgr文件。
5. trait_list_paper.txt：收录本论文分析的70种疾病/性状的列表。
6. ldspec_results.zip：包含70种疾病/性状的LDSPEC分析结果。

此外，其余数据文件存放于独立文件夹中：
- 连锁不平衡评分与方向连锁不平衡评分：https://figshare.com/account/projects/188052/articles/24716901
- 全基因组关联研究（Genome-Wide Association Study, GWAS）汇总统计数据：https://figshare.com/account/projects/188052/articles/24716952