SNP and SNP-set results for low-density lipoprotein (LDL) cholesterol in individuals assayed within the Framingham Heart Study.

We analyze J = 394,174 SNPs and G = 18, 364 SNP-sets from N = 6,950 people. Here, SNP-set annotations are based on gene boundaries defined by the NCBI’s RefSeq database in the UCSC Genome Browser [50]. Unannotated SNPs located within the same genomic region were labeled as being within the “intergenic region” between two genes. This file gives the posterior inclusion probabilities (PIPs) for the input and hidden layer neural network weights after fitting the BANNs model on the individual-level data. We assess significance for both SNPs and SNP-sets according to the “median probability model” threshold [57] (i.e., PIP ≥ 0.5). Page #1 provides the variant-level association mapping results with columns corresponding to: (1) chromosome; (2) SNP ID; (3) chromosomal position in base-pair (bp) coordinates; (4) SNP PIP; and (5) SuSiE PIP, which corresponds to SNP-level posterior inclusion probabilities computed by SuSiE [46]. Page #2 provides the SNP-set level enrichment results with columns corresponding to: (1) chromosome; (2) SNP-set ID; (3-4) the starting and ending position of the SNP-set chromosomal boundaries; (5) SNP-set PIP; (6) RSS PIP, which corresponds to the posterior inclusion probabilities computed by RSS [26]; (7) the number of SNPs that have been annotated within each SNP-set; (8) the “top” associated SNP within each SNP-set; (9) the PIP of each top SNP. Pages #3 and #4 provide similar results based on analyses where each SNP-set annotation has been augmented with a ±500 kilobase (kb) buffer to account for possible regulatory elements.
(ZIP)

我们对来自N=6950名个体的J=394174个单核苷酸多态性（Single Nucleotide Polymorphism，SNP）以及G=18364个SNP集合（SNP-set）开展分析。本研究中的SNP集合注释基于UCSC基因组浏览器中NCBI的RefSeq数据库所定义的基因边界[50]。位于同一基因组区域且未被注释的SNP将被标记为两个基因之间的"基因间区"。
本文件提供了在个体水平数据上拟合BANNs模型后，输入层与隐藏层神经网络权重的后包含概率（posterior inclusion probability，PIP）。我们依据"中位数概率模型"阈值[57]（即PIP≥0.5）对SNP及SNP集合的显著性进行评估。
第1页提供了变异水平的关联定位结果，各列依次对应：(1) 染色体编号；(2) SNP ID；(3) 以碱基对（bp）为单位的染色体坐标位置；(4) SNP的PIP；以及(5) SuSiE PIP，即由SuSiE[46]计算得到的SNP水平后包含概率。
第2页提供了SNP集合水平的富集分析结果，各列依次对应：(1) 染色体编号；(2) SNP集合ID；(3-4) SNP集合染色体边界的起始与终止位置；(5) SNP集合的PIP；(6) RSS PIP，即由RSS[26]计算得到的后包含概率；(7) 每个SNP集合内已注释的SNP数量；(8) 每个SNP集合内的"最优"关联SNP；(9) 该最优关联SNP的PIP。
第3页与第4页提供了基于另一组分析的相似结果，该分析中每个SNP集合注释均附加了±500千碱基对（kb）的缓冲区域，以覆盖可能存在的调控元件。
(ZIP)