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LOC129932994 ATAC-STARR-seq lymphoblastoid active region 15228 [ Homo sapiens (human) ]

Gene ID: 129932994, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932994
Gene description
ATAC-STARR-seq lymphoblastoid active region 15228
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 LOC129932994 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 (3377622..3377801)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (3399743..3399922)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (3381393..3381572)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1250 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3105730-3106514 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:3108292-3108999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3112467-3113140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3118175-3118676 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3131179-3131343 Neighboring gene uncharacterized LOC107985840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3172751-3173696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3182069-3182826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3183585-3184342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3184343-3185098 Neighboring gene Sharpr-MPRA regulatory region 8446 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:3202367-3202905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3204190-3204746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15224 Neighboring gene MPRA-validated peak3584 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:3237853-3239052 Neighboring gene EARP complex and GARP complex interacting protein 1 Neighboring gene Sharpr-MPRA regulatory region 3808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15226 Neighboring gene VISTA enhancer hs1385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3284251-3284751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3289510-3290088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3290089-3290666 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3310431-3310601 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3323251-3323862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3326607-3327134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3327135-3327662 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3358809-3358982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11108 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3382431-3382947 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3381914-3382430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11109 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3402817-3403742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3403743-3404668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3404669-3405592 Neighboring gene trafficking protein particle complex subunit 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3416341-3416841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3415840-3416340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3434408-3434908 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3437307-3437557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3463593-3464106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3464459-3465326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3475415-3475916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3475917-3476416 Neighboring gene TRAPPC12 antisense RNA 1 Neighboring gene uncharacterized LOC112268321

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_166019.1 

    Range
    101..280
    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
    3377622..3377801
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    3399743..3399922
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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