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LOC130061824 ATAC-STARR-seq lymphoblastoid active region 12887 [ Homo sapiens (human) ]

Gene ID: 130061824, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061824
Gene description
ATAC-STARR-seq lymphoblastoid active region 12887
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 LOC130061824 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (78276247..78276516)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (79170368..79170637)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (76272328..76272597)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene transmembrane protein 235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12882 Neighboring gene MPRA-validated peak3016 silencer Neighboring gene uncharacterized LOC105371910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76246144-76246789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12883 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76249484-76250202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76250203-76250920 Neighboring gene CRISPRi-validated cis-regulatory element chr17.5434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12886 Neighboring gene CRISPRi-validated cis-regulatory element chr17.5435 Neighboring gene threonine aldolase 1, pseudogene Neighboring gene long intergenic non-protein coding RNA 1993 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76263321-76264044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76264045-76264770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76266221-76266945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76268313-76269002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76273439-76274272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76274273-76275106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76283739-76284240 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:76287812-76288081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76297857-76298375 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:76304459-76304681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9056 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76311214-76311972 Neighboring gene uncharacterized LOC105371912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12890 Neighboring gene Sharpr-MPRA regulatory region 775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76318420-76318963 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76320051-76320592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76320593-76321136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76321137-76321678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9058 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9059 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9060 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76338363-76338868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76340895-76341399 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9061 Neighboring gene uncharacterized LOC124904064 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76348009-76348824 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76348825-76349641

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_196936.1 

    Range
    101..370
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    78276247..78276516
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    79170368..79170637
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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