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LOC128462409 CRISPRi-FlowFISH-validated IL10 regulatory element GRCh37_chr1:206945468-206946089 [ Homo sapiens (human) ]

Gene ID: 128462409, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128462409
Gene description
CRISPRi-FlowFISH-validated IL10 regulatory element GRCh37_chr1:206945468-206946089
Gene type
biological region
Feature type(s)
regulatory: transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region, which includes the 5' end of the IL10 (interleukin 10) gene, was predicted to be an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. It was validated as a positively-acting cis-regulatory element for IL10 (interleukin 10) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in unstimulated BJAB lymphoma cells. A subregion was also validated as an IL10 regulatory element by CRISPRi-FlowFISH in anti-CD40- and anti-IgM-stimulated BJAB lymphoma cells. This genomic region is of relevance to coronavirus biology because the IL10 target gene is involved in the cytokine storm inflammatory response to viral infection. [provided by RefSeq, Feb 2023]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is involved in host gene regulation.
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Genomic context

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See LOC128462409 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (206772123..206772744)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (206036324..206036945)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904496 Neighboring gene uncharacterized LOC124904495 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1762 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1763 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1764 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:206860855-206861416 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:206861417-206861978 Neighboring gene MAPK activated protein kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2412 Neighboring gene ribosomal protein S14 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 3087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:206895773-206896486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1765 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2417 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:206937123-206937321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2420 Neighboring gene interleukin 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2422 Neighboring gene interleukin 19 Neighboring gene CRISPRi-FlowFISH-validated IL10 regulatory elements GRCh37_chr1:206966528-206967028 and GRCh37_chr1:206966531-206967031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1767 Neighboring gene uncharacterized LOC105372878 Neighboring gene interleukin 20

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genome-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

General gene information

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Other Names

  • CRISPRi-FlowFISH-validated IL10 regulatory element GRCh37_chr1:206945550-206946089

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_149597.1 

    Range
    101..722
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    206772123..206772744
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    206036324..206036945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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