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LOC117125598 CRISPRi-FlowFISH-validated PRDX2 regulatory element 7 [ Homo sapiens (human) ]

Gene ID: 117125598, updated on 10-Oct-2023

Summary

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Gene symbol
LOC117125598
Gene description
CRISPRi-FlowFISH-validated PRDX2 regulatory element 7
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 negatively-acting cis-regulatory element for the PRDX2 (peroxiredoxin 2) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. [provided by RefSeq, Mar 2020]
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Genomic context

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See LOC117125598 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13191111..13191611)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13316370..13316870)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13301925..13302425)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14114 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13263956-13264839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14121 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13276087-13276664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13278116-13278743 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13280436-13280936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13280937-13281437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14123 Neighboring gene ribosomal protein L12 pseudogene 42 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14124 Neighboring gene OCT4 hESC enhancer GRCh37_chr19:13295659-13296160 Neighboring gene Sharpr-MPRA regulatory region 13602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13297074-13297984 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13297985-13298895 Neighboring gene immediate early response 2 Neighboring gene MPRA-validated peak3367 silencer Neighboring gene calcium voltage-gated channel subunit alpha1 A repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10203 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13319630-13320530 Neighboring gene MPRA-validated peak3368 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13335615-13336116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13336117-13336616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13337139-13337640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13341838-13342338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13342339-13342839 Neighboring gene calcium voltage-gated channel subunit alpha1 A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10204 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:13371552-13372751 Neighboring gene Sharpr-MPRA regulatory region 13658 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:13385818-13387017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14132 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:13445719-13446918 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:13509521-13510720 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:13511134-13511634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:13511635-13512135 Neighboring gene Sharpr-MPRA regulatory region 1233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13618335-13618861 Neighboring gene uncharacterized LOC107985287

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. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Fulco CP, et al. Nat Genet, 2019 Dec. PMID 31784727, 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

See Variation Viewer (GRCh37.p13)

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_068136.1 

    Range
    101..601
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    13191111..13191611
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    13316370..13316870
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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