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LOC129997271 ATAC-STARR-seq lymphoblastoid active region 25147 [ Homo sapiens (human) ]

Gene ID: 129997271, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997271
Gene description
ATAC-STARR-seq lymphoblastoid active region 25147
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 LOC129997271 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 (137811732..137811851)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (139000156..139000275)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (138132869..138132988)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17586 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:138039958-138040164 Neighboring gene PTPN11 pseudogene 3 Neighboring gene long intergenic non-protein coding RNA 2539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17587 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25151 Neighboring gene wound and keratinocyte migration associated lncRNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25154 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:138196296-138197495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:138200115-138200697 Neighboring gene TNF alpha induced protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25156 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:138246817-138248016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25157 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17592 Neighboring gene long intergenic non-protein coding RNA 2865 Neighboring gene suppressor of inflammatory macrophage apoptosis lncRNA

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_176717.1 

    Range
    101..220
    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
    137811732..137811851
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    139000156..139000275
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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