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LOC130005561 ATAC-STARR-seq lymphoblastoid active region 4619 [ Homo sapiens (human) ]

Gene ID: 130005561, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005561
Gene description
ATAC-STARR-seq lymphoblastoid active region 4619
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 LOC130005561 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (35166029..35166088)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (35304092..35304151)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (35187576..35187635)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:35159883-35160447 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:35161615-35162115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4618 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:35173058-35173288 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:35173309-35174101 Neighboring gene CD44 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3257 Neighboring gene CD44 molecule (IN blood group) Neighboring gene NANOG hESC enhancer GRCh37_chr11:35194606-35195107 Neighboring gene small nucleolar RNA, C/D box 164 Neighboring gene NANOG hESC enhancer GRCh37_chr11:35227049-35227813 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:35235787-35236986 Neighboring gene NANOG hESC enhancer GRCh37_chr11:35238494-35239323 Neighboring gene CD44 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4622 Neighboring gene solute carrier family 1 member 2 Neighboring gene SLC1A2 antisense RNA 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_185006.1 

    Range
    101..160
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    35166029..35166088
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    35304092..35304151
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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