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LOC116309128 CRISPRi-validated cis-regulatory element chr22.1058 [ Homo sapiens (human) ]

Gene ID: 116309128, updated on 12-Sep-2024

Summary

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Gene symbol
LOC116309128
Gene description
CRISPRi-validated cis-regulatory element chr22.1058
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 represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. It was validated as a high-confidence cis-regulatory element for the TPST2 (tyrosylprotein sulfotransferase 2) gene on chromosome 22 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
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Genomic context

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See LOC116309128 in Genome Data Viewer
Location:
22q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (26632476..26633226)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (27095093..27095843)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (27028440..27029190)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene tyrosylprotein sulfotransferase 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:26959537-26960060 Neighboring gene hESC enhancers GRCh37_chr22:26963727-26964250 and GRCh37_chr22:26964251-26964774 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:26964775-26965298 Neighboring gene high mobility group box 1 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18793 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr22:26975739-26976656 and GRCh37_chr22:26976657-26977573 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:26985294-26985794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:27003362-27004004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13574 Neighboring gene crystallin beta A4 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:27009656-27010334 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27013045-27013722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27014401-27015076 Neighboring gene crystallin beta B1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27037805-27038669 Neighboring gene Sharpr-MPRA regulatory region 8650 Neighboring gene Sharpr-MPRA regulatory region 12592 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27041123-27041688 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27043802-27044604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27045408-27046209 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18797 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr22:27057049-27058028 Neighboring gene iron-sulfur cluster assembly 2 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:27061097-27061597 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27063956-27064539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27064540-27065122 Neighboring gene myocardial infarction associated transcript Neighboring gene MIAT neighbor

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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, 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_067097.1 

    Range
    101..851
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    26632476..26633226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    27095093..27095843
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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