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LOC129995528 ATAC-STARR-seq lymphoblastoid active region 23807 [ Homo sapiens (human) ]

Gene ID: 129995528, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995528
Gene description
ATAC-STARR-seq lymphoblastoid active region 23807
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 LOC129995528 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (225435..225594)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (80381..80540)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (225435..225594)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ankyrin repeat domain 18F, pseudogene Neighboring gene long intergenic non-protein coding RNA 3066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23798 Neighboring gene lincRNA regulator of IL2RA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23812 Neighboring gene uncharacterized LOC105374870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23814 Neighboring gene MPRA-validated peak5614 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr6:281277-281431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23816 Neighboring gene H3K27ac hESC enhancers GRCh37_chr6:291666-292166 and GRCh37_chr6:292167-292667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23818 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:293614-293770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23822 Neighboring gene dual specificity phosphatase 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16804 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:314342-314521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:324055-324866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23829 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:329543-330742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23831 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:342926-343426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23835

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_174974.1 

    Range
    101..260
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    225435..225594
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    80381..80540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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