how could snps contribute to gene regulation?

As such, the three-dimensional (3D) genome organization, which emerges from the sum of the biophysical interactions within the nucleus, includes tissue-specific spatial interactions between eQTL regions and the genes that they control (hereafter eGenes)12. As such, the genes we identified need not directly overlap those that have been previously curated as being involved in ASD through deletion or mutation studies. 2022 Sep 16;13:942643. doi: 10.3389/fneur.2022.942643. Collectively, our results provide insight into potential cortex-specific regulatory mechanisms and pathways through which ASD-associated SNPs can contribute to the development and maintenance of ASD. how could SNP's contribute to gene regulation? Louvain clustering analysis identified seven highly connected PPI modules within fetal cortex. Maurano, M. T. et al. https://doi.org/10.1038/s41588-022-01087-y, Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity. Finally a number of fetal (n=50) and adult (n=28) cortex-specific eQTLs were observed (Supplementary Table 3). SNP alleles in human disease and evolution. Finally, we evaluated identified eQTL SNP associations with other phenotypes in the GWAS Catalog (downloaded on 26/08/2020) (Supplementary Table 4). 370, 12091219 (2014). Fetal and adult ASD-associated eQTLs were also associated with schizophrenia, unipolar depression, ADHD, bipolar disorder, anorexia nervosa and obsessivecompulsive disorder (Supplementary Fig. 2009 May;37(5):977-91. doi: 10.1124/dmd.108.026047. RNA-seq data)20,21 were mapped to gene identifiers, thus there was a potential loss of data specificity, since genes typically produce multiple transcripts and protein variants due to alternative splicing. PPI network analyses have been used to discover essential proteins, clusters of proteins with similar, overlapping or combinatorial functions, and associated pathways involved in tissue-specific contributions to ASD etiology17,18. & Wang, K. wANNOVAR: Annotating genetic variants for personal genomes via the web. Genet. Nat Genet 54, 748749 (2022). HHS Vulnerability Disclosure, Help [34] Genome-wide genetic data can be generated by multiple technologies, including SNP array and whole genome sequencing. 2a, Supplementary Table 3). By contrast, the adult cortical gene set was largely related to immune pathways. Article The patterns of transcript changes in the adult cortex PPI network were similar to those observed in the fetal cortex. 4, 334336 (2011). Nat. Mol. Finucane, H. K. et al. Neuron 89, 248268 (2016). Won, H. et al. A new study highlights a strategy to link SNPs implicated in human complex traits and diseases with probable causal genes. Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. Explaining the disease phenotype of intergenic SNP through - PubMed Golovina, E., Fadason, T., Lints, T.J. et al. Walker, R. L. et al. A compendium of chromatin contact maps reveals spatially active regions in the human genome. The identified ASD-associated eQTLs were annotated using wANNOVAR tool77 (http://wannovar.wglab.org/, 10/08/2020) to obtain information about the locus they tagged (Supplementary Table 4). Nat. 19, 13211330 (2016). This will revolutionize the medical field in the future.