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This article will explain in detail what is the use of 3dsnp database for you. The editor thinks it is very practical, so I share it with you for reference. I hope you can get something after reading this article.

Among the SNP loci in the whole genome, the SNP loci located on the coding genes are only a very small part, and most of them are located in the non-coding region. Through ENCODE, Roadmap and other projects, we have obtained the positional relationship between SNP loci and various elements of the genome. However, it is very difficult to explain and predict the role of SNPs in gene regulation only through location distribution. Similar to the regulatory role of enhancers, gene regulation is a very complex process, not only between elements with similar genomic locations.

With the development of three-dimensional genomics, especially the discovery of chromatin ring structure, people have a better understanding of the mechanism of gene regulation. The chromatin ring shortens the distance between the enhancer and the promoter in space, so that the enhancer can combine with the promoter, thus breaking through the limitation of linear distance and playing a regulatory role.

In order to better study the relationship between SNP and gene regulation, scientists linked chromatin ring-mediated interaction information with SNP, and mined and sorted out the distribution of SNP loci located in the non-coding region in the spatial interaction through the public database.

The web address of the database is as follows

Http://cbportal.org/3dsnp/

The SNP locus information of human was obtained from dbSNP database, and then the linkage relationship between SNP loci was obtained by LD analysis of frequencies in 1000G database. At the same time, we annotate the genes near the SNP site, and use the gene annotation provided by UCSC to annotate the genes in the range of 2kb on both sides of the upstream and downstream of the SNP site.

For the chromatin spatial interaction information, the chromatin ring information is obtained directly from the published hi-c data. If the original hi-c data set does not provide chromatin ring information, the chromatin ring is analyzed by HOMER software.

Combining the genomic location of chromatin ring and SNP loci, the distribution of SNP loci in the regulatory network mediated by chromatin ring can be constructed. In order to further study the effect of SNP on the regulatory network, the corresponding enhancers, promoters, transcription factor binding sites, motif and other annotation information of SNP are also provided.

At the same time, in order to better screen SNP sites, combined with a variety of annotation information mentioned above, a scoring system was established to score the importance of SNP sites in the regulatory network.

The search can be easily carried out through the search box on the front page, and the search results are as follows

Click SNP ID to view the details. Take rs746077852 as an example, the results are as follows

1. Summary information

This section shows the scores of the SNP locus, as shown below

2. Genomic location and frequency of SNP locus

3. Visualization of distribution on the genome

Two visualization results, circos and UCSC, are provided as follows

4. Linear closest gene

Genes within the range of 2kb upstream and downstream of SNP locus, as shown below

5. Distribution in the chromatin ring

6. Distribution in enhancer and promoter

7. Inter-species conservation

3dSNP database links SNP loci with chromatin ring-mediated regulation information, which provides a new perspective for SNP research, and provides a new idea for studying the effects of SNP on gene regulation, which is worthy of reference.

This is the end of this article on "what is the use of 3dsnp database?". I hope the above content can be of some help to you, so that you can learn more knowledge. if you think the article is good, please share it for more people to see.

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