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LOC126859756 BRD4-independent group 4 enhancer GRCh37_chr6:106582537-106583736 [ Homo sapiens (human) ]

Gene ID: 126859756, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126859756
Gene description
BRD4-independent group 4 enhancer GRCh37_chr6:106582537-106583736
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay. The major subregion had activity in HCT116 colorectal carcinoma cells, where it was defined as a group 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. Two subregions marked by the H3K4me1 histone modification were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. [provided by RefSeq, Oct 2022]
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Genomic context

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See LOC126859756 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (106134282..106135861)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (107310139..107311718)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17429 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106441121-106441655 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:106442725-106443257 Neighboring gene NANOG hESC enhancer GRCh37_chr6:106462748-106463464 Neighboring gene PR/SET domain 1 Neighboring gene NANOG hESC enhancer GRCh37_chr6:106511809-106512319 Neighboring gene NANOG hESC enhancer GRCh37_chr6:106528405-106528951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24877 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:106533839-106534558 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:106546043-106547242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:106553364-106554077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:106552649-106553363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24878 Neighboring gene Sharpr-MPRA regulatory region 9287 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106611080-106611926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106611927-106612773 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:106614661-106615396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17430 Neighboring gene MPRA-validated peak6001 silencer Neighboring gene autophagy related 5 Neighboring gene RNA, 7SL, cytoplasmic 47, pseudogene Neighboring gene RNA, U6 small nuclear 344, pseudogene

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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K4me1 hESC enhancer GRCh37_chr6:106582157-106582658
  • H3K4me1 hESC enhancer GRCh37_chr6:106582659-106583158

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_084257.2 

    Range
    101..1680
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    106134282..106135861
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    107310139..107311718
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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