HaploReg

HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects, sequence conservation across mammals, the effect of SNPs on regulatory motifs, and the effect of SNPs on expression from eQTL studies. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.HaploReg是一款用于探索单倍型区块上变异位点的非编码基因组注释信息的工具，可用于解析疾病关联位点上的候选调控单核苷酸多态性（Single Nucleotide Polymorphism, SNP）。借助千人基因组计划（1000 Genomes Project）提供的连锁不平衡（Linkage Disequilibrium, LD）信息，该工具可对关联SNPs与小型插入缺失变异（insertion-deletion, indel）进行可视化展示，同时呈现来自表观基因组路线图计划（Roadmap Epigenomics）与DNA元件百科全书计划（Encyclopedia of DNA Elements, ENCODE）的染色质状态及蛋白质结合注释、哺乳动物跨物种序列保守性、SNPs对调控基序的影响，以及基于表达数量性状位点（expression Quantitative Trait Locus, eQTL）研究得到的SNPs对基因表达的调控效应。HaploReg专为致力于构建非编码变异对临床表型与正常变异影响机制假说的科研人员设计。

搜集汇总

背景与挑战

背景概述

HaploReg是一个用于探索非编码基因组变体注释的工具，专注于单倍型块上的变异，如疾病相关SNPs。它整合了多种数据源，包括LD信息、染色质状态和eQTL研究结果，旨在支持研究人员分析非编码变异对临床表型和正常变异的影响。