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LOC130004952 ATAC-STARR-seq lymphoblastoid active region 4201 [ Homo sapiens (human) ]

Gene ID: 130004952, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004952
Gene description
ATAC-STARR-seq lymphoblastoid active region 4201
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 LOC130004952 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (128126683..128126912)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (129025215..129025444)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (129924947..129925176)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase receptor type E Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:129860232-129861431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129861772-129862370 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:129867603-129867800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129876157-129876658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129876659-129877158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129889651-129890152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129890153-129890652 Neighboring gene lncRNA antisense to PTPRE protein-coding gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2933 Neighboring gene NANOG hESC enhancer GRCh37_chr10:129963700-129964282 Neighboring gene marker of proliferation Ki-67 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:129970982-129972181 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:129999872-130000380 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:130000381-130000888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130007752-130008313 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130109218-130109718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130109719-130110219 Neighboring gene uncharacterized LOC124902558 Neighboring gene long intergenic non-protein coding RNA 1163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130184885-130185386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130232943-130233444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130238232-130238732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130281853-130282352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130281351-130281852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:130317555-130318446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:130318447-130319337 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:130339525-130340200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130365840-130366340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130366341-130366841 Neighboring gene VISTA enhancer hs737 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:130424650-130424847 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:130427109-130428308 Neighboring gene uncharacterized LOC105378554

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_184397.1 

    Range
    101..330
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    128126683..128126912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    129025215..129025444
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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