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LOC129934096 ATAC-STARR-seq lymphoblastoid active region 16036 [ Homo sapiens (human) ]

Gene ID: 129934096, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934096
Gene description
ATAC-STARR-seq lymphoblastoid active region 16036
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 LOC129934096 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (73926912..73927181)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (73935379..73935648)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (74154039..74154308)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene zinc finger DHHC-type palmitoyltransferase 6 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74119211-74120024 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:74139533-74139680 Neighboring gene actin gamma 2, smooth muscle Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74164465-74164964 Neighboring gene deoxyguanosine kinase Neighboring gene DGUOK antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16037 Neighboring gene RNA, 5S ribosomal pseudogene 97 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74210413-74211336 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:74211958-74212156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16041 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11649 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74230812-74231328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74231329-74231844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74235869-74236827 Neighboring gene tet methylcytosine dioxygenase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74248449-74248948 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74252809-74253686 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:74253687-74254564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74257891-74258392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74258393-74258892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16044 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:74259869-74260014 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:74278831-74279332 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:74279333-74279832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74312841-74313340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74326577-74327076 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16045 Neighboring gene formin binding protein 1 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_167120.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    73926912..73927181
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    73935379..73935648
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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