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LOC130067153 ATAC-STARR-seq lymphoblastoid active region 18794 [ Homo sapiens (human) ]

Gene ID: 130067153, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067153
Gene description
ATAC-STARR-seq lymphoblastoid active region 18794
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 LOC130067153 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (26590347..26590486)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (27052679..27052818)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (26986311..26986450)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene tyrosylprotein sulfotransferase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:26951753-26952722 Neighboring gene microRNA 548j Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:26959537-26960060 Neighboring gene high mobility group box 1 pseudogene 10 Neighboring gene hESC enhancers GRCh37_chr22:26963727-26964250 and GRCh37_chr22:26964251-26964774 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:26964775-26965298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18793 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr22:26975739-26976656 and GRCh37_chr22:26976657-26977573 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:26985294-26985794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18795 Neighboring gene crystallin beta A4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:27003362-27004004 Neighboring gene crystallin beta B1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13574 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:27009656-27010334 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27013045-27013722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27014401-27015076 Neighboring gene CRISPRi-validated cis-regulatory element chr22.1058 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27037805-27038669 Neighboring gene Sharpr-MPRA regulatory region 8650 Neighboring gene Sharpr-MPRA regulatory region 12592 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27041123-27041688 Neighboring gene iron-sulfur cluster assembly 2 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_201568.1 

    Range
    101..240
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    26590347..26590486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    27052679..27052818
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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