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LOC129930480 ATAC-STARR-seq lymphoblastoid active region 999 [ Homo sapiens (human) ]

Gene ID: 129930480, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129930480
Gene description
ATAC-STARR-seq lymphoblastoid active region 999
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 LOC129930480 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (46340668..46340877)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (46217886..46218095)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (46806340..46806549)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RAD54 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46750956-46751580 Neighboring gene leucine rich repeat containing 41 Neighboring gene NANOG hESC enhancer GRCh37_chr1:46764257-46764758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46766628-46767210 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46767211-46767793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 844 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:46768959-46769542 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:46769543-46770124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 998 Neighboring gene ubiquinol-cytochrome c reductase hinge protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46794429-46795157 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:46795158-46795887 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46795888-46796616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46797347-46798076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 845 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:46804880-46805679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1000 Neighboring gene NOP2/Sun RNA methyltransferase 4 Neighboring gene MPRA-validated peak205 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr1:46837735-46837899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46859877-46860390 Neighboring gene fatty acid amide hydrolase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1001 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:46898417-46899137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1003 Neighboring gene fatty acid amide hydrolase 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_163531.1 

    Range
    101..310
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    46340668..46340877
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    46217886..46218095
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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