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LOC130001397 ATAC-STARR-seq lymphoblastoid active region 28098 [ Homo sapiens (human) ]

Gene ID: 130001397, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001397
Gene description
ATAC-STARR-seq lymphoblastoid active region 28098
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 LOC130001397 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144413292..144413341)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145583105..145583154)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (145638676..145638725)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene cleavage and polyadenylation specific factor 1 Neighboring gene microRNA 1234 Neighboring gene microRNA 6849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19682 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145638844-145639041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145639267-145640084 Neighboring gene uncharacterized LOC124902041 Neighboring gene solute carrier family 39 member 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145647393-145648164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145648165-145648934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145651263-145652026 Neighboring gene VPS28 subunit of ESCRT-I Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19684

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_180843.1 

    Range
    101..150
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    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    144413292..144413341
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654716.1 Reference GRCh38.p14 PATCHES

    Range
    143895..143944
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    145583105..145583154
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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