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LOC129996254 ATAC-STARR-seq lymphoblastoid active region 24411 [ Homo sapiens (human) ]

Gene ID: 129996254, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996254
Gene description
ATAC-STARR-seq lymphoblastoid active region 24411
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 LOC129996254 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 (35720503..35720742)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (35540871..35541110)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (35688280..35688519)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene FKBP prolyl isomerase 5 Neighboring gene small nucleolar RNA SNORA40 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:35630473-35630974 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:35630975-35631474 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:35639883-35640082 Neighboring gene microRNA 5690 Neighboring gene MPRA-validated peak5774 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17096 Neighboring gene MPRA-validated peak5775 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35685276-35685841 Neighboring gene Sharpr-MPRA regulatory region 8621 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:35693619-35693795 Neighboring gene Sharpr-MPRA regulatory region 11861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24412 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17098 Neighboring gene Sharpr-MPRA regulatory region 7900 Neighboring gene uncharacterized LOC285847 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35705089-35705697 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35705698-35706306 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35706915-35707523 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35707524-35708131 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:35715250-35715449 Neighboring gene armadillo repeat containing 12 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:35723005-35723594 Neighboring gene MPRA-validated peak5777 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24413 Neighboring gene MPRA-validated peak5778 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24414 Neighboring gene CMPK1 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_175700.1 

    Range
    101..340
    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
    35720503..35720742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    35540871..35541110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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