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LOC129992053 ATAC-STARR-seq lymphoblastoid active region 21180 [ Homo sapiens (human) ]

Gene ID: 129992053, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129992053
Gene description
ATAC-STARR-seq lymphoblastoid active region 21180
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 LOC129992053 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (2712312..2712531)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (2711078..2711297)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (2714039..2714258)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374353 Neighboring gene uncharacterized LOC107986250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15170 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:2470739-2471311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2478879-2479379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2480295-2480819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21176 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:2487795-2488296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2491261-2492041 Neighboring gene ring finger protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15176 Neighboring gene Sharpr-MPRA regulatory region 6001 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2556971-2557807 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2557808-2558643 Neighboring gene family with sequence similarity 193 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2561739-2562277 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2597477-2598429 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2598430-2599381 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2599382-2600334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2620021-2620522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2625441-2626235 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2632219-2632720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2632721-2633220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2648543-2649043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2660247-2660748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2660749-2661248 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2672935-2673479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2746569-2747069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15179 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2763311-2764135 Neighboring gene uncharacterized LOC102723763 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2764939-2765507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21183 Neighboring gene TNFAIP3 interacting protein 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_171499.1 

    Range
    101..320
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    2712312..2712531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    2711078..2711297
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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