Input SNP-Level Summary Data

Completed on: Sun Apr 09 21:20:47 2023 (Asia/Shanghai), with the runtime of (53 seconds).

An interactive table for user-input SNPs (n=216, being processed). This table has three columns: 1st column SNPs for dbSNP rsIDs (hyperlinked to dbSNP), 2nd column P-values for use-input significance information, and 3rd column Locus for genomic locations (the genome build hg19).

Output: Linked Genes

Linked Gene table contains information on genes (n=407, linked from the input SNPs), including the column GScores (ranged from 1 to 10) that quantifies the degree to which genes are responsible for genetic associations. Linked genes are sorted by their linked gene scores and are hyperlinked to GeneCards for further information. Please refer to Evidence table for details on the linking evidence.

Evidence table displays information on which SNPs (see the column SNPs) are used to define linked genes (the column Linked genes) based on which evidence (see the column Evidence). The column SNP type indicates whether the SNP is an input SNP (Input) or an additional SNP in linkage disequilibrium (LD). The column Evidence contains information on the datasets used, such as Proximity (indicative of SNPs in proximity), the prefix PCHiC_ (promoter capture Hi-C datasets), and the prefix eQTL_ or pQTL_ (e/pQTL datasets).

Output: Gene Subnetwork

A network visualisation of the subnetwork, with 31 genes/nodes color-coded by linked gene scores (ranged from 1 to 10). An editable pdf file is also available for download.

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Visualisation of the identified subnetwork, with genes/nodes color-coded by linked gene scores (ranged from 1 to 10).

Figure 1: Visualisation of the identified subnetwork, with genes/nodes color-coded by linked gene scores (ranged from 1 to 10).

An interactive table for the subnetwork genes (n=31), with the column GScores for linked gene scores (ranged from 1 to 10). Each gene listed in the column Linked genes is hyperlinked to its corresponding GeneCards page.