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LOC129995846 ATAC-STARR-seq lymphoblastoid active region 24052 [ Homo sapiens (human) ]

Gene ID: 129995846, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995846
Gene description
ATAC-STARR-seq lymphoblastoid active region 24052
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 LOC129995846 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (14661195..14661274)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (14533606..14533685)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (14661426..14661505)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374942 Neighboring gene uncharacterized LOC101928331 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:14441647-14442345 Neighboring gene NANOG hESC enhancer GRCh37_chr6:14450188-14450778 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:14472912-14473412 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:14473413-14473913 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:14474901-14475125 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:14508670-14509869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14540385-14540955 Neighboring gene uncharacterized LOC101928354 Neighboring gene Sharpr-MPRA regulatory region 399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24051 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:14639937-14640920 Neighboring gene uncharacterized LOC102724463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24053 Neighboring gene RNA, U6 small nuclear 793, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14676877-14677412 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:14706129-14707328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24054 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:14730658-14731857 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:14733080-14734279 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16945 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:14743342-14744541 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14784175-14784726 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr6:14784727-14785278 and GRCh37_chr6:14785279-14785830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14804615-14805450 Neighboring gene Sharpr-MPRA regulatory region 9195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24056 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14823177-14823964 Neighboring gene NANOG hESC enhancer GRCh37_chr6:14822305-14822806 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14824752-14825538 Neighboring gene NANOG hESC enhancer GRCh37_chr6:14832080-14832596 Neighboring gene Sharpr-MPRA regulatory region 9180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24057 Neighboring gene uncharacterized LOC105374945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14876936-14877436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14879976-14880486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14880487-14880996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14883452-14884163 Neighboring gene MPRA-validated peak5674 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24062 Neighboring gene MPRA-validated peak5675 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr6:14958411-14958600 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:14997283-14997782 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15013597-15013834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15017607-15018302 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15021466-15022336 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15022337-15023206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24063 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:15066479-15067678 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15077925-15078456 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15096502-15096739 Neighboring gene ribosomal protein L6 pseudogene 17

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_175292.1 

    Range
    101..180
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    14661195..14661274
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    14533606..14533685
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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