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LOC129996583 ATAC-STARR-seq lymphoblastoid active region 24647 [ Homo sapiens (human) ]

Gene ID: 129996583, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996583
Gene description
ATAC-STARR-seq lymphoblastoid active region 24647
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 LOC129996583 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 (45924306..45924455)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (45759738..45759887)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (45892043..45892192)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RUNX2 antisense RNA 1 Neighboring gene U6 spliceosomal RNA Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:45623433-45624632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24646 Neighboring gene NANOG hESC enhancer GRCh37_chr6:45669242-45669749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17267 Neighboring gene Sharpr-MPRA regulatory region 1586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45722353-45722853 Neighboring gene VISTA enhancer hs1461 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:45866604-45867157 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:45868755-45869954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45894464-45895128 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:45895129-45895792 Neighboring gene chloride intracellular channel 5 Neighboring gene uncharacterized LOC124901326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45928377-45928876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45982710-45983554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45983555-45984399 Neighboring gene RNA, U6 small nuclear 754, pseudogene

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_176029.1 

    Range
    101..250
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    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
    45924306..45924455
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    45759738..45759887
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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