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LOC129997248 ATAC-STARR-seq lymphoblastoid active region 25128 [ Homo sapiens (human) ]

Gene ID: 129997248, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997248
Gene description
ATAC-STARR-seq lymphoblastoid active region 25128
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 LOC129997248 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 (137076646..137076855)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (138264421..138264630)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (137397783..137397992)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:137311375-137312331 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:137322965-137323508 Neighboring gene neuroblastoma highly expressed DDX5 stabilizing lncRNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90349 Neighboring gene interleukin 20 receptor subunit alpha Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17577 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17578 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17579 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:137382319-137382457 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:137410449-137410629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25131 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90355 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25133 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90359 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90362 Neighboring gene interleukin 22 receptor subunit alpha 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:137492881-137493639 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90370 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:137500946-137502145 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17580 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:137540162-137540892 Neighboring gene interferon gamma receptor 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_176694.1 

    Range
    101..310
    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
    137076646..137076855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    138264421..138264630
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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