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LOC129995741 ATAC-STARR-seq lymphoblastoid active region 23967 [ Homo sapiens (human) ]

Gene ID: 129995741, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995741
Gene description
ATAC-STARR-seq lymphoblastoid active region 23967
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 LOC129995741 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 (10521638..10521697)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (10389346..10389405)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (10521871..10521930)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:10466572-10467078 Neighboring gene long intergenic non-protein coding RNA 2522 Neighboring gene uncharacterized LOC101928146 Neighboring gene glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group) pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:10518715-10519215 Neighboring gene NFE2L2 motif-containing MPRA enhancer 266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:10519455-10520150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23969 Neighboring gene glucosaminyl (N-acetyl) transferase 2 (I blood group) Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:10555959-10556854 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:10558788-10559335 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:10559462-10560216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:10564953-10565514 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:10575275-10575920 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:10575921-10576566 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:10576567-10577212 Neighboring gene Sharpr-MPRA regulatory region 5327 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:10582905-10583878 Neighboring gene ribosomal protein L21 pseudogene 63 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:10585827-10586799 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:10589255-10589802 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:10596165-10597152 Neighboring gene GCNT2 pseudogene 1

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_175187.1 

    Range
    101..160
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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
    10521638..10521697
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654713.1 Reference GRCh38.p14 PATCHES

    Range
    32522..32581
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    10389346..10389405
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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