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LOC129997806 ATAC-STARR-seq lymphoblastoid active region 25524 [ Homo sapiens (human) ]

Gene ID: 129997806, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997806
Gene description
ATAC-STARR-seq lymphoblastoid active region 25524
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 LOC129997806 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 (2312181..2312350)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (2425679..2425848)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (2351816..2351985)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2297547-2298326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2298327-2299106 Neighboring gene microRNA 6836 Neighboring gene sorting nexin 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2309692-2310302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2310912-2311521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2311522-2312130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25520 Neighboring gene inner mitochondrial membrane peptidase subunit 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25521 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2340879-2341379 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2341882-2342382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2349114-2349623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2349624-2350134 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:2350135-2350643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17865 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:2354180-2354680 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:2354681-2355181 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2393253-2393808 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17869 Neighboring gene eukaryotic translation initiation factor 3 subunit B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2416395-2416894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:2418983-2419483 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:2429085-2429981 Neighboring gene kinesin family member 19B, pseudogene

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_177247.1 

    Range
    101..270
    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
    2312181..2312350
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    2425679..2425848
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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