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LOC130063877 ATAC-STARR-seq lymphoblastoid active region 14231 [ Homo sapiens (human) ]

Gene ID: 130063877, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063877
Gene description
ATAC-STARR-seq lymphoblastoid active region 14231
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 LOC130063877 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (16417695..16417744)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (16552508..16552557)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (16528506..16528555)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:16435432-16436204 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:16436205-16436975 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14224 Neighboring gene KLF transcription factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14226 Neighboring gene epidermal growth factor receptor pathway substrate 15 like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14228 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:16486555-16487056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14229 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:16494079-16494580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:16528701-16529304 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:16531117-16531720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:16531721-16532324 Neighboring gene ribosomal protein S2 pseudogene 51 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:16551872-16552372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:16552373-16552873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14232 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:16555578-16556777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:16564379-16564879 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:16565415-16565914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:16567358-16568116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:16572441-16573108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:16573109-16573776 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:16575487-16576411 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:16581959-16582870 Neighboring gene Sharpr-MPRA regulatory region 3003 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:16606242-16606742 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:16606743-16607243 Neighboring gene calreticulin 3 Neighboring gene chromosome 19 open reading frame 44 Neighboring gene calcium homeostasis endoplasmic reticulum protein

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_198294.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    16417695..16417744
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    16552508..16552557
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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