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LOC130061813 ATAC-STARR-seq lymphoblastoid active region 12876 [ Homo sapiens (human) ]

Gene ID: 130061813, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061813
Gene description
ATAC-STARR-seq lymphoblastoid active region 12876
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 LOC130061813 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (78175433..78175612)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (79069527..79069706)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (76171514..76171693)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene chromosome 17 open reading frame 99 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76154005-76154506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9049 Neighboring gene eukaryotic translation initiation factor 5A pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76160142-76160642 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9050 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12875 Neighboring gene synaptogyrin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12877 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76171843-76172621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76172622-76173399 Neighboring gene thymidine kinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76180346-76181247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9052 Neighboring gene arylformamidase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12879 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:76207979-76208182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76210079-76210980 Neighboring gene baculoviral IAP repeat containing 5

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_196927.1 

    Range
    101..280
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    78175433..78175612
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    79069527..79069706
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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