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LOC129999474 ATAC-STARR-seq lymphoblastoid active region 26762 [ Homo sapiens (human) ]

Gene ID: 129999474, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999474
Gene description
ATAC-STARR-seq lymphoblastoid active region 26762
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 LOC129999474 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (139494973..139495022)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (140808266..140808315)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (139179719..139179768)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene FMC1-LUC7L2 readthrough Neighboring gene LUC7 like 2, pre-mRNA splicing factor Neighboring gene uncharacterized LOC100129148 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:139111514-139112150 Neighboring gene killer cell lectin like receptor G2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139136252-139137140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:139137141-139138027 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:139138916-139139802 Neighboring gene RNA, U6 small nuclear 911, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:139146664-139147433 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:139150055-139150776 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:139152221-139152942 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:139153665-139154386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139154387-139155106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139164064-139164564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:139164565-139165065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26763 Neighboring gene ST13, Hsp70 interacting protein pseudogene 17 Neighboring gene C-type lectin domain family 2 member L Neighboring gene ERH 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_178920.1 

    Range
    101..150
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    139494973..139495022
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    140808266..140808315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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