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LOC130058408 ATAC-STARR-seq lymphoblastoid active region 10367 [ Homo sapiens (human) ]

Gene ID: 130058408, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130058408
Gene description
ATAC-STARR-seq lymphoblastoid active region 10367
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 LOC130058408 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (8960030..8960099)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (8992698..8992767)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (9053887..9053956)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7181 Neighboring gene CARHSP1 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr16:8971783-8971898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10357 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:8976345-8976845 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:8981773-8982615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10360 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:8997705-8998206 Neighboring gene LITAF domain containing Neighboring gene ubiquitin specific peptidase 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10364 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:9047245-9048444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10365 Neighboring gene Sharpr-MPRA regulatory region 8678 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:9056134-9056670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7183 Neighboring gene hESC enhancers GRCh37_chr16:9059367-9059990 and GRCh37_chr16:9059991-9060614 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:9060615-9061236 Neighboring gene USP7 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:9077187-9078074 Neighboring gene Sharpr-MPRA regulatory region 2468 Neighboring gene Sharpr-MPRA regulatory region 11265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:9102552-9103123 Neighboring gene Sharpr-MPRA regulatory region 10025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:9120319-9120818 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:9141017-9142216 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:9143640-9144432 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:9144433-9145223 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:9146779-9147316 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:9161527-9162726 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:9183666-9184531 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:9191093-9191592 Neighboring gene HUWE1 associated protein modifying stress responses Neighboring gene Sharpr-MPRA regulatory region 1845

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_192829.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    8960030..8960099
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    8992698..8992767
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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