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LOC121466694 Sharpr-MPRA regulatory region 8178 [ Homo sapiens (human) ]

Gene ID: 121466694, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121466694
Gene description
Sharpr-MPRA regulatory region 8178
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 was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, May 2021]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (47753486..47753780)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (47714802..47715096)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48147269..48147563)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6256 Neighboring gene RNA polymerase II associated protein 3 Neighboring gene H3K27ac hESC enhancers GRCh37_chr12:48099027-48099528 and GRCh37_chr12:48099529-48100028 Neighboring gene RPAP3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6258 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6259 Neighboring gene endonuclease, poly(U) specific Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4394 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4395 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:48131928-48133127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6261 Neighboring gene Rap guanine nucleotide exchange factor 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:48146243-48146784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48151874-48152542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48152543-48153211 Neighboring gene solute carrier family 48 member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48167242-48167748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48167749-48168253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4399 Neighboring gene histone deacetylase 7 Neighboring gene uncharacterized LOC124902926

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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_074625.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    47753486..47753780
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    47714802..47715096
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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