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LOC116309129 CRISPRi-validated cis-regulatory element chr22.1165 [ Homo sapiens (human) ]

Gene ID: 116309129, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116309129
Gene description
CRISPRi-validated cis-regulatory element chr22.1165
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 cis-regulatory element for the EMID1 (EMI domain containing 1) 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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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (29195471..29196309)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (29658972..29659807)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (29591459..29592297)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene kringle containing transmembrane protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:29536985-29537486 Neighboring gene RNA, U6 small nuclear 810, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:29537487-29537986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:29541773-29542473 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:29547849-29548632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18810 Neighboring gene uncharacterized LOC101929638 Neighboring gene RNA, U6 small nuclear 1219, pseudogene Neighboring gene Sharpr-MPRA regulatory region 4816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:29610708-29611288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:29611289-29611868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:29611869-29612448 Neighboring gene uncharacterized LOC124905099 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:29612449-29613028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:29613609-29614188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:29614189-29614768 Neighboring gene uncharacterized LOC105372985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:29619669-29620170 Neighboring gene EMI domain containing 1

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_067098.1 

    Range
    101..939
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    29195471..29196309
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    29658972..29659807
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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