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LOC129931823 ATAC-STARR-seq lymphoblastoid active region 2025 [ Homo sapiens (human) ]

Gene ID: 129931823, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129931823
Gene description
ATAC-STARR-seq lymphoblastoid active region 2025
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 LOC129931823 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (166170176..166170255)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (165516204..165516283)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (166139413..166139492)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 78 member B Neighboring gene FAM78B antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_946 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:166097641-166098142 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_966 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_978 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:166135105-166136007 Neighboring gene uncharacterized LOC112268276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1509 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1510 Neighboring gene microRNA 921 Neighboring gene EWS RNA binding protein 1 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr1:166276066-166276742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:166312727-166313227 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:166322051-166322217 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:166352300-166353120 Neighboring gene long intergenic non-protein coding RNA 1675 Neighboring gene flavin containing dimethylaniline monoxygenase 7, 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_164866.1 

    Range
    101..180
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    166170176..166170255
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    165516204..165516283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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