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LOC129995875 ATAC-STARR-seq lymphoblastoid active region 24076 [ Homo sapiens (human) ]

Gene ID: 129995875, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995875
Gene description
ATAC-STARR-seq lymphoblastoid active region 24076
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 LOC129995875 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 (15335955..15336104)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (15209150..15209295)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (15336186..15336335)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene jumonji and AT-rich interaction domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24074 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16951 Neighboring gene RNA, U6 small nuclear 522, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15337209-15337728 Neighboring gene RNA, U6 small nuclear 645, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15385480-15386240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24079 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15402869-15403369 Neighboring gene Sharpr-MPRA regulatory region 1760 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15404593-15405283 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15413673-15413840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24081 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15444755-15445255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15447999-15448499 Neighboring gene NANOG hESC enhancer GRCh37_chr6:15461204-15461861 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15469722-15469904 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:15473668-15474867 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:15491921-15492422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15507577-15508118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15508119-15508660 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:15508661-15509202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15513022-15514000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15517558-15518058 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15523265-15523451 Neighboring gene uncharacterized LOC105374947 Neighboring gene MPRA-validated peak5680 silencer Neighboring gene Sharpr-MPRA regulatory region 14615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15551965-15552513 Neighboring gene dystrobrevin binding protein 1 Neighboring gene DTNBP1 antisense RNA 1

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_175321.1 

    Range
    101..250
    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
    15335955..15336104
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    15209150..15209295
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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