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LOC130061893 ATAC-STARR-seq lymphoblastoid active region 12926 [ Homo sapiens (human) ]

Gene ID: 130061893, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061893
Gene description
ATAC-STARR-seq lymphoblastoid active region 12926
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 LOC130061893 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 (79942898..79943177)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (80840829..80841108)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (77916697..77916976)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77809787-77810608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9092 Neighboring gene Sharpr-MPRA regulatory region 202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12923 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77811431-77812254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77812255-77813076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77814721-77815544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77815545-77816366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9095 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:77824032-77825231 Neighboring gene chromobox 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12924 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:77842993-77843520 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:77843521-77844050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77862335-77862836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77875585-77876566 Neighboring gene long intergenic non-protein coding RNA 1979 Neighboring gene long intergenic non-protein coding RNA 1978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77917109-77917834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77917835-77918560 Neighboring gene TBC1 domain family member 16 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77921171-77921997 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77922367-77922950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77922951-77923534 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77923535-77924118 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77924703-77925286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77925287-77925870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77930057-77930557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77948310-77949214 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:77951994-77952173 Neighboring gene uncharacterized LOC124904073 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77961646-77962517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9097 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:77966696-77967895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77975818-77976678 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:77987013-77987179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77996703-77997568 Neighboring gene uncharacterized LOC124904072

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_196994.1 

    Range
    101..380
    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
    79942898..79943177
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    80840829..80841108
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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