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LOC130056319 ATAC-STARR-seq lymphoblastoid active region 8913 [ Homo sapiens (human) ]

Gene ID: 130056319, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056319
Gene description
ATAC-STARR-seq lymphoblastoid active region 8913
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 LOC130056319 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (91398328..91398397)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (85623568..85623637)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (91864672..91864741)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91710745-91711246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91719939-91720470 Neighboring gene G protein-coupled receptor 68 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91720471-91721002 Neighboring gene CRISPRi-validated cis-regulatory element chr14.1904 Neighboring gene Sharpr-MPRA regulatory region 4292 Neighboring gene CRISPRi-validated cis-regulatory element chr14.1906 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:91749514-91749720 Neighboring gene coiled-coil domain containing 88C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6023 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91771631-91772466 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91772467-91773300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91818809-91819780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91821242-91821752 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:91826469-91826970 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:91826971-91827470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8910 Neighboring gene uncharacterized LOC107984673 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91838097-91838709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8911 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:91841845-91842517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91843867-91844540 Neighboring gene uncharacterized LOC105370624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6025 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91848585-91849375 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91849376-91850165 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91853480-91854308 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91854309-91855135 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91864835-91865466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91866728-91867357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91884645-91885289 Neighboring gene COX assembly mitochondrial protein homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8921 Neighboring gene CCDC88C divergent transcript Neighboring gene uncharacterized LOC124903361

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_190740.1 

    Range
    101..170
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    91398328..91398397
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    85623568..85623637
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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