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LOC123575656 NANOG-H3K4me1 hESC enhancer GRCh37_chr6:3511328-3512180 [ Homo sapiens (human) ]

Gene ID: 123575656, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575656
Gene description
NANOG-H3K4me1 hESC enhancer GRCh37_chr6:3511328-3512180
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. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K4me1 histone modification. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC123575656 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 (3511094..3511946)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (3379837..3380689)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (3511689..3511983)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 22 member 23 Neighboring gene HNF4 motif-containing MPRA enhancer 213 Neighboring gene uncharacterized LOC105374890 Neighboring gene Sharpr-MPRA regulatory region 2334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3413621-3414120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3415185-3415686 Neighboring gene Sharpr-MPRA regulatory region 10234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:3427759-3428672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23892 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:3446415-3446962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:3446963-3447509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16853 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16854 Neighboring gene Sharpr-MPRA regulatory region 3383 Neighboring gene uncharacterized LOC643327 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:3490051-3490550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3540364-3540864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3563205-3563704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3568820-3569322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3579367-3580278 Neighboring gene uncharacterized LOC100507336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3603461-3603960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3724209-3724747 Neighboring gene TOMM5 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 15708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3737712-3738338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16855 Neighboring gene PX 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. 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

  • Sharpr-MPRA regulatory region 10864

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_077915.2 

    Range
    101..953
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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
    3511094..3511946
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    3379837..3380689
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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