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LOC129996954 ATAC-STARR-seq lymphoblastoid active region 24920 [ Homo sapiens (human) ]

Gene ID: 129996954, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996954
Gene description
ATAC-STARR-seq lymphoblastoid active region 24920
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 LOC129996954 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (109094214..109094363)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (110272321..110272470)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (109415417..109415566)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene armadillo repeat containing 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:109241738-109242648 Neighboring gene ARMC2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109266564-109267120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109272427-109272928 Neighboring gene MPRA-validated peak6016 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24919 Neighboring gene sestrin 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:109367051-109367618 Neighboring gene Sharpr-MPRA regulatory region 5156 Neighboring gene RNA, U6 small nuclear 653, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24921 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:109422661-109423052 Neighboring gene centrosomal protein 57 like 1 Neighboring gene coiled-coil domain containing 162, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109515122-109515622 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:109562791-109563990 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:109572150-109572928 Neighboring gene uncharacterized LOC124901374

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_176400.1 

    Range
    101..250
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    109094214..109094363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    110272321..110272470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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