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LOC129996420 ATAC-STARR-seq lymphoblastoid active region 24520 [ Homo sapiens (human) ]

Gene ID: 129996420, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996420
Gene description
ATAC-STARR-seq lymphoblastoid active region 24520
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 LOC129996420 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 (41716333..41716382)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (41544890..41544939)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (41684071..41684120)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41608279-41608859 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:41612529-41613514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41614501-41615485 Neighboring gene MyoD family inhibitor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41625153-41625767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41641529-41642028 Neighboring gene nucleophosmin 1 pseudogene 51 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41642607-41643108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41644810-41645324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41645325-41645838 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41649993-41650819 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41650820-41651645 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41655149-41656015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41658364-41658864 Neighboring gene transcription factor EB Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41673380-41673880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41673881-41674381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24519 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41680541-41681266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41681267-41681990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41690842-41691384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41700542-41701238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17189 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17190 Neighboring gene microRNA 10398 Neighboring gene progastricsin

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_175866.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    41716333..41716382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    41544890..41544939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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