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LOC130068699 ATAC-STARR-seq lymphoblastoid active region 29957 [ Homo sapiens (human) ]

Gene ID: 130068699, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130068699
Gene description
ATAC-STARR-seq lymphoblastoid active region 29957
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 LOC130068699 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 (131747035..131747094)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (130071282..130071341)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (130881063..130881122)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 2 subfamily AF member 1 pseudogene Neighboring gene heparin binding growth factor pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:130798263-130798901 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29949 Neighboring gene Sharpr-MPRA regulatory region 5272 Neighboring gene firre intergenic repeating RNA element Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:130851242-130851768 Neighboring gene MPRA-validated peak7427 silencer Neighboring gene NANOG hESC enhancer GRCh37_chrX:130854476-130855009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29962 Neighboring gene Sharpr-MPRA regulatory region 13451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29964 Neighboring gene Sharpr-MPRA regulatory region 4069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:130937096-130937596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:130937597-130938097 Neighboring gene MAPK regulated corepressor interacting protein 2 pseudogene 1 Neighboring gene PNKD pseudogene 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_203113.1 

    Range
    101..160
    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
    131747035..131747094
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    130071282..130071341
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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