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LOC128462383 CRISPRi-FlowFISH-validated IL2RA regulatory element GRCh37_chr10:6094489-6094989 [ Homo sapiens (human) ]

Gene ID: 128462383, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128462383
Gene description
CRISPRi-FlowFISH-validated IL2RA regulatory element GRCh37_chr10:6094489-6094989
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 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 the IL2RA (interleukin 2 receptor subunit alpha) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in anti-CD3- and PMA-stimulated Jurkat T cells. The IL2RA target gene is relevant for COVID-19 prognosis. [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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Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (6052526..6053026)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (6053219..6053717)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902368 Neighboring gene small nucleolar RNA SNORA14 Neighboring gene interleukin 2 receptor subunit alpha Neighboring gene uncharacterized LOC107984201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2950 Neighboring gene CRISPRi-FlowFISH-validated IL2RA regulatory element GRCh37_chr10:6104083-6104713 Neighboring gene MPRA-validated peak860 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2951 Neighboring gene ribosomal protein L32 pseudogene 23 Neighboring gene CRISPRi-FlowFISH-validated IL2RA regulatory element GRCh37_chr10:6125624-6126124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2098 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:6131655-6132493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6137781-6138282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6138283-6138782 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:6138886-6139486 Neighboring gene RNA binding motif protein 17 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:6149773-6150468 Neighboring gene MPRA-validated peak861 silencer

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

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_149571.1 

    Range
    101..601
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    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    6052526..6053026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    6053219..6053717
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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