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LOC127819979 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:449779-450465 [ Homo sapiens (human) ]

Gene ID: 127819979, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127819979
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:449779-450465
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 region includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC127819979 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (449779..450613)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (495123..495957)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (449779..450613)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:405522-406215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2999 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:415472-416091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3003 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3004 Neighboring gene single Ig and TIR domain containing Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:420870-421731 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:428546-429745 Neighboring gene uncharacterized LOC105376506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:434102-434620 Neighboring gene anoctamin 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3005 Neighboring gene Sharpr-MPRA regulatory region 223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:442612-443409 Neighboring gene RNA, 7SL, cytoplasmic 838, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4275 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:454927-455648 Neighboring gene phosphatidylserine synthase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:460662-460845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:467161-467660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:471334-471857 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:471858-472380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:476893-477888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:484337-484858 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:487868-488008 Neighboring gene MPRA-validated peak1145 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21531 Neighboring gene ribonuclease/angiogenin inhibitor 1 Neighboring gene leucine rich repeat containing 56 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:528505-529042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:533792-534649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:534650-535506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:535528-536235 Neighboring gene HRas proto-oncogene, GTPase

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 4276
  • ATAC-STARR-seq lymphoblastoid silent region 3008

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_121446.2 

    Range
    101..935
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    449779..450613
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    495123..495957
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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