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LOC130066008 ATAC-STARR-seq lymphoblastoid active region 17992 [ Homo sapiens (human) ]

Gene ID: 130066008, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066008
Gene description
ATAC-STARR-seq lymphoblastoid active region 17992
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 LOC130066008 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (47410408..47410597)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (49148683..49148872)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (46039152..46039341)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene zinc finger MYND-type containing 8 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45947067-45947983 Neighboring gene uncharacterized LOC100131496 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45947984-45948902 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45950739-45951656 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:45957753-45958400 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:45959988-45960488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45964446-45965285 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45965286-45966124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:45968129-45968628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45971039-45971820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45974595-45975341 Neighboring gene uncharacterized LOC101927377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17984 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45983444-45984051 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45985267-45985874 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45986483-45987088 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr20:45987089-45987696 and GRCh37_chr20:45987697-45988304 Neighboring gene CRISPRi-validated cis-regulatory element chr20.2033 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46001472-46002090 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46005195-46005694 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46004693-46005194 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46007335-46007835 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46012139-46012991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17991 Neighboring gene long intergenic non-protein coding RNA 1754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46044799-46045298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46057414-46057914 Neighboring gene MPRA-validated peak4230 silencer Neighboring gene MPRA-validated peak4231 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17995 Neighboring gene Sharpr-MPRA regulatory region 10107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17996 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:46108400-46108953 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46108954-46109506 Neighboring gene RNA, U6 small nuclear 497, pseudogene Neighboring gene ribosomal protein L35a pseudogene

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 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_200425.1 

    Range
    101..290
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    47410408..47410597
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    49148683..49148872
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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