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LOC129996002 ATAC-STARR-seq lymphoblastoid active region 24171 [ Homo sapiens (human) ]

Gene ID: 129996002, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996002
Gene description
ATAC-STARR-seq lymphoblastoid active region 24171
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 LOC129996002 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 (25992776..25992985)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (25858715..25858924)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (25993004..25993213)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 17 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24170 Neighboring gene CRISPRi-validated cis-regulatory element chr6.1077 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:25971247-25972446 Neighboring gene tripartite motif containing 38 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16997 Neighboring gene long intergenic non-protein coding RNA 2980 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:25999111-25999745 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:25999746-26000381 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:26016208-26017207 Neighboring gene H3 histone pseudogene 26 Neighboring gene H1.1 linker histone, cluster member

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 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_175448.1 

    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
    25992776..25992985
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    25858715..25858924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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