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LOC129999095 ATAC-STARR-seq lymphoblastoid active region 26474 [ Homo sapiens (human) ]

Gene ID: 129999095, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999095
Gene description
ATAC-STARR-seq lymphoblastoid active region 26474
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 LOC129999095 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (105808916..105808985)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (107123495..107123564)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (105449362..105449431)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene EFCAB10 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105221332-105221844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105221845-105222355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26467 Neighboring gene Sharpr-MPRA regulatory region 14983 Neighboring gene EF-hand calcium binding domain 10 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105241179-105241956 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105255907-105256408 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105256409-105256908 Neighboring gene Y-box binding protein 1 pseudogene 2 Neighboring gene ataxin 7 like 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105279303-105279964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105281471-105282438 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:105288402-105288618 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:105288629-105289828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105293127-105293850 Neighboring gene Sharpr-MPRA regulatory region 7350 Neighboring gene Sharpr-MPRA regulatory region 5075 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105316356-105316856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105319379-105320318 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105321123-105321622 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105329021-105329696 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105329697-105330372 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105330373-105331048 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:105331049-105331724 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105331725-105332400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105335755-105336518 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:105337283-105338044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26470 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105409403-105409904 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105409905-105410404 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:105412749-105413248 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:105416274-105417473 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:105423855-105424084 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105428411-105428946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105432252-105432810 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105432811-105433367 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:105434917-105436116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105437186-105437686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26475 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:105470396-105471595 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105477786-105478643 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105478644-105479500 Neighboring gene ribosomal protein L13a pseudogene 16 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105494345-105495094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18524 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:105525198-105525381 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:105528806-105529002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105596161-105596662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:105596663-105597162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105602263-105603214 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105603215-105604166 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:105631053-105631700 Neighboring gene uncharacterized LOC107986833 Neighboring gene cadherin related family member 3

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_178541.1 

    Range
    101..170
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    105808916..105808985
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    107123495..107123564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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