U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123575647 hESC enhancers GRCh37_chr6:2907997-2908830 and GRCh37_chr6:2908831-2909664 [ Homo sapiens (human) ]

Gene ID: 123575647, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123575647
Gene description
hESC enhancers GRCh37_chr6:2907997-2908830 and GRCh37_chr6:2908831-2909664
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 were validated as active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where both are marked by the H3K27ac histone modification, and one is additionally marked by H3K4me1 and the other is associated with the NANOG transcription factor. An overlapping subregion was also validated as a functional repressive element 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 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Oct 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC123575647 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (2907763..2909430)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (2774001..2775672)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (2908689..2908983)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23876 Neighboring gene serpin family B member 9 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23879 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2869952-2870526 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2875298-2876239 Neighboring gene SERPINB9 antisense RNA 1 Neighboring gene MPRA-validated peak5624 silencer Neighboring gene serpin family B member 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16834 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2903007-2903508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16836 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16837 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:2916616-2917158 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:2921833-2922334 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:2928364-2929022 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2929023-2929682 Neighboring gene serpin family B member 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2960063-2960678 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2971582-2972106 Neighboring gene SERPINB6-LINC01011 intergenic CAGE-defined mid-level expression enhancer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2988143-2988952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2988953-2989762 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2989763-2990572 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2990573-2991380 Neighboring gene long intergenic non-protein coding RNA 1011 Neighboring gene NQO2 antisense RNA 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:2907997-2908830
  • NANOG-H3K27ac hESC enhancer GRCh37_chr6:2908831-2909664
  • Sharpr-MPRA regulatory region 12972

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_077906.2 

    Range
    101..1768
    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
    2907763..2909430
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    2774001..2775672
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases