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LOC129932042 ATAC-STARR-seq lymphoblastoid active region 2187 [ Homo sapiens (human) ]

Gene ID: 129932042, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932042
Gene description
ATAC-STARR-seq lymphoblastoid active region 2187
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 LOC129932042 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (181424773..181424862)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (180780187..180780276)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (181393909..181393998)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak492 silencer Neighboring gene long intergenic non-protein coding RNA 1699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181277357-181277857 Neighboring gene uncharacterized LOC107985454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181287535-181288165 Neighboring gene calcium voltage-gated channel subunit alpha1 E Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2185 Neighboring gene uncharacterized LOC107985232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1611 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2189 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181450844-181451376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181452360-181452884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:181452885-181453408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2193 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2194 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:181598156-181598432 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:181737037-181738236 Neighboring gene RNA, 5S ribosomal pseudogene 70 Neighboring gene RN7SK pseudogene 229

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 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_165084.1 

    Range
    101..190
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    181424773..181424862
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    180780187..180780276
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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