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LOC129994115 ATAC-STARR-seq lymphoblastoid active region 22713 [ Homo sapiens (human) ]

Gene ID: 129994115, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994115
Gene description
ATAC-STARR-seq lymphoblastoid active region 22713
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 represents an accessible chromatin region that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC129994115 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (78573433..78573482)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (79054927..79054976)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (77869256..77869305)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77655493-77656089 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77656090-77656686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16120 Neighboring gene SCAMP1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:77687375-77687953 Neighboring gene secretory carrier membrane protein 1 Neighboring gene MPRA-validated peak5302 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77753154-77753763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77788199-77788702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22709 Neighboring gene Sharpr-MPRA regulatory region 4849 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77800693-77801201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16121 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77805941-77806562 Neighboring gene LHFPL tetraspan subfamily member 2 Neighboring gene Sharpr-MPRA regulatory region 4833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77828783-77829282 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77838469-77839288 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77839289-77840106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22711 Neighboring gene Sharpr-MPRA regulatory region 10457 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:77911679-77912878 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:77922186-77922385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77928669-77929170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77929171-77929670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16123 Neighboring gene uncharacterized LOC124900191 Neighboring gene high mobility group box 1 pseudogene 21 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:77995230-77996429 Neighboring gene Sharpr-MPRA regulatory region 2428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22719

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

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)

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_173561.1 

    Range
    101..150
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    78573433..78573482
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    79054927..79054976
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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