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LOC130068598 ATAC-STARR-seq lymphoblastoid active region 29883 [ Homo sapiens (human) ]

Gene ID: 130068598, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130068598
Gene description
ATAC-STARR-seq lymphoblastoid active region 29883
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 LOC130068598 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (119638692..119638811)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (118016422..118016541)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (118772655..118772774)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:118708298-118708798 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:118708799-118709299 Neighboring gene ubiquitin conjugating enzyme E2 A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29882 Neighboring gene NFKB repressing factor Neighboring gene septin 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29886 Neighboring gene microRNA 766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:118811626-118812126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20966 Neighboring gene sosondowah ankyrin repeat domain family member D

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_203012.1 

    Range
    101..220
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    119638692..119638811
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791817.1 Reference GRCh38.p14 PATCHES

    Range
    89694..89813
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    118016422..118016541
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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