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LOC121740641 H3K27ac-H3K4me1 hESC enhancers GRCh37_chr6:11770721-11771242 and GRCh37_chr6:11771243-11771766 [ Homo sapiens (human) ]

Gene ID: 121740641, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121740641
Gene description
H3K27ac-H3K4me1 hESC enhancers GRCh37_chr6:11770721-11771242 and GRCh37_chr6:11771243-11771766
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. Two subregions marked by the H3K27ac and H3K4me1 histone modifications were validated as active enhancers by ChIP-STARR-seq in human embryonic stem cells. An overlapping subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (11770488..11771533)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (11638699..11639744)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (11771129..11771423)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC340184 Neighboring gene small nucleolar RNA SNORA67 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23991 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:11722447-11723646 Neighboring gene uncharacterized LOC124901258 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88259 Neighboring gene androgen dependent TFPI regulating protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23993 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:11763549-11763791 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11770197-11770720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11794232-11794800 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11794801-11795369 Neighboring gene uncharacterized LOC107986567 Neighboring gene uncharacterized LOC124901257 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:11834142-11834332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23994 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:11838380-11838562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23997 Neighboring gene uncharacterized LOC102724379 Neighboring gene adenosylmethionine decarboxylase 1 pseudogene 4

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-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11770721-11771242
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:11771243-11771766
  • Sharpr-MPRA regulatory region 14499

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_075703.2 

    Range
    101..1146
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    11770488..11771533
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    11638699..11639744
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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