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LOC121466723 Sharpr-MPRA regulatory region 11163 [ Homo sapiens (human) ]

Gene ID: 121466723, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121466723
Gene description
Sharpr-MPRA regulatory region 11163
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [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 (122112122..122112416)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (122107909..122108203)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (122596669..122596963)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5004 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122460343-122461158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7197 Neighboring gene BAF chromatin remodeling complex subunit BCL7A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122492684-122493298 Neighboring gene Sharpr-MPRA regulatory region 9922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7198 Neighboring gene Sharpr-MPRA regulatory region 8907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122509410-122510254 Neighboring gene long intergenic non-protein coding RNA 2985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122580754-122581254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122581255-122581755 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122582507-122583160 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122583161-122583814 Neighboring gene MLX interacting protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7205 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122611084-122611596 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122611597-122612107 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:122614034-122615233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122622713-122623575 Neighboring gene MPRA-validated peak2016 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122651061-122651663 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5010 Neighboring gene leucine rich repeat containing 43 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7209 Neighboring gene interleukin 31 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5011 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4 Neighboring gene diablo IAP-binding mitochondrial protein

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_074656.1 

    Range
    101..395
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    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
    122112122..122112416
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332697.1 Reference GRCh38.p14 PATCHES

    Range
    53079..53373
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    122107909..122108203
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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