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LOC112694727 Sharpr-MPRA regulatory region 13995 [ Homo sapiens (human) ]

Gene ID: 112694727, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112694727
Gene description
Sharpr-MPRA regulatory region 13995
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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. A subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes three accessible chromatin subregions that were validated as silencers based on their ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC112694727 in Genome Data Viewer
Location:
20q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63553341..63553730)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65365938..65366327)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62184694..62185083)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13159 Neighboring gene protein tyrosine kinase 6 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18227 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62175449-62176002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62178175-62178816 Neighboring gene src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13164 Neighboring gene fibronectin type III domain containing 11 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18230 Neighboring gene helicase with zinc finger 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18233 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18232 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62202570-62202926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13165 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62205701-62206428 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62207026-62207211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62213946-62214446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62214447-62214947 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61137 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61148 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61158 Neighboring gene glucocorticoid modulatory element binding protein 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61169 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61181 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61184 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18235 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62250681-62251180 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13168

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 13161
  • ATAC-STARR-seq lymphoblastoid silent region 13162
  • ATAC-STARR-seq lymphoblastoid silent region 13163

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_060756.2 

    Range
    101..490
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    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    63553341..63553730
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65365938..65366327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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