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LOC129996307 ATAC-STARR-seq lymphoblastoid active region 24449 [ Homo sapiens (human) ]

Gene ID: 129996307, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996307
Gene description
ATAC-STARR-seq lymphoblastoid active region 24449
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 LOC129996307 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 (37007621..37007790)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (36831005..36831174)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (36975397..36975566)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36926417-36926918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36926919-36927418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36930796-36931421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36931422-36932046 Neighboring gene peptidase inhibitor 16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36948504-36949104 Neighboring gene mitochondrial carrier 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:36953526-36954248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24447 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:36960675-36960875 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36965399-36966022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36966023-36966646 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:36973029-36973191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36979647-36980146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36981577-36982294 Neighboring gene FYVE, RhoGEF and PH domain containing 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:36992286-36993485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24450 Neighboring gene CRISPRi-validated cis-regulatory element chr6.2470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24451 Neighboring gene COX6A1 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37024071-37024957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:37025005-37025506 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:37025507-37026006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17126 Neighboring gene Sharpr-MPRA regulatory region 8589 Neighboring gene Sharpr-MPRA regulatory region 8119 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37045201-37045729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37051359-37051859 Neighboring gene ribosomal protein L12 pseudogene 2

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_175753.1 

    Range
    101..270
    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
    37007621..37007790
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    36831005..36831174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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