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LOC129997221 ATAC-STARR-seq lymphoblastoid active region 25104 [ Homo sapiens (human) ]

Gene ID: 129997221, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997221
Gene description
ATAC-STARR-seq lymphoblastoid active region 25104
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 LOC129997221 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 (135234243..135234312)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (136422497..136422566)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (135555381..135555450)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25100 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:135491500-135491716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17563 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25102 Neighboring gene Sharpr-MPRA regulatory region 12483 Neighboring gene uncharacterized LOC105378011 Neighboring gene MYB proto-oncogene, transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25103 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:135570900-135572099 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:135573042-135573542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:135573543-135574043 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:135577907-135579106 Neighboring gene microRNA 548a-2 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:135585007-135585209 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:135591948-135592842 Neighboring gene VISTA enhancer hs1351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25105 Neighboring gene CRISPRi-validated MYB cis-regulatory element XLOC_042889 Neighboring gene uncharacterized LOC124901407 Neighboring gene Sharpr-MPRA regulatory region 12318 Neighboring gene Abelson helper integration site 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_176667.1 

    Range
    101..170
    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
    135234243..135234312
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    136422497..136422566
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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