LOC106096416 (KRT18 locus control region) - Rat Genome Database

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Gene: LOC106096416 (KRT18 locus control region) Homo sapiens
Analyze
Symbol: LOC106096416
Name: KRT18 locus control region
RGD ID: 38661502
Description: This region contains multiple positive and negative regulatory elements spanning the KRT18 (keratin 18) gene region, which function together to control the tissue-specific, copy number dependent, and integration-site independent expression of KRT18. These elements include a 5' opposite orientation Alu element, whose transcription is required to modulate copy number dependent expression of the adjacent gene. The Alu element can also function independently as an enhancer, insulator, and enhancer blocker, depending on the context. Additional positive regulatory elements in this region include a cryptic promoter upstream of the canonical KRT18 promoter, an enhancer within the first intron, and a regulatory element in the sixth exon. Activity of the element in the sixth exon can be disrupted by a frameshifting mutation that decreases the stability of the KRT18 transcript. A subregion overlapping the 5' portion of the gene was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where both are associated with the NANOG transcription factor and are marked by the H3K27ac and H3K4me1 histone modifications. Another subregion located upstream of the gene was also validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands). 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]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381252,947,765 - 52,956,706 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371253,341,823 - 53,350,490 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map12q13NCBI
T2T-CHM13v2.01252,912,321 - 52,921,248 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:1696235   PMID:1697294   PMID:2454392   PMID:2469635   PMID:7508123   PMID:7526151   PMID:7537848   PMID:7667273   PMID:7680099   PMID:7681143   PMID:7692231   PMID:8730098  
PMID:9271368   PMID:9346889   PMID:9405675   PMID:9756890   PMID:10625605   PMID:11356077   PMID:27701403   PMID:30033119   PMID:35650434   PMID:35858748  


Genomics

Variants

.
Variants in LOC106096416
37 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_000224.3(KRT18):c.268C>T (p.Arg90Cys) single nucleotide variant not provided [RCV001572635]|not specified [RCV001729957] Chr12:52949441 [GRCh38]
Chr12:53343225 [GRCh37]
Chr12:12q13.13		 benign|likely benign
NM_000224.3(KRT18):c.300C>G (p.Ser100Arg) single nucleotide variant not provided [RCV001572658]|not specified [RCV001729958] Chr12:52949473 [GRCh38]
Chr12:53343257 [GRCh37]
Chr12:12q13.13		 benign|likely benign
NM_000224.3(KRT18):c.274G>C (p.Ala92Pro) single nucleotide variant not provided [RCV001572633]|not specified [RCV001729956] Chr12:52949447 [GRCh38]
Chr12:53343231 [GRCh37]
Chr12:12q13.13		 benign|likely benign
GRCh38/hg38 12q13.13(chr12:52748391-52950618)x3 copy number gain See cases [RCV000138642] Chr12:52748391..52950618 [GRCh38]
Chr12:53142175..53344402 [GRCh37]
Chr12:51428442..51630669 [NCBI36]
Chr12:12q13.13		 likely benign
NM_000224.3(KRT18):c.1232G>A (p.Arg411His) single nucleotide variant not provided [RCV000056432] Chr12:52952781 [GRCh38]
Chr12:53346565 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.827A>G (p.Glu276Gly) single nucleotide variant not provided [RCV000056441] Chr12:52951735 [GRCh38]
Chr12:53345519 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.383A>T (p.His128Leu) single nucleotide variant Cirrhosis, cryptogenic [RCV000015686]|Cirrhosis, noncryptogenic, susceptibility to [RCV000015687]|not provided [RCV000056435] Chr12:52949556 [GRCh38]
Chr12:53343340 [GRCh37]
Chr12:12q13.13		 pathogenic|risk factor|not provided
NM_000224.3(KRT18):c.854A>G (p.Gln285Arg) single nucleotide variant not provided [RCV000056442] Chr12:52951762 [GRCh38]
Chr12:53345546 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.1018G>A (p.Gly340Arg) single nucleotide variant not provided [RCV000056431] Chr12:52952188 [GRCh38]
Chr12:53345972 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.193_216del (p.Thr65_Ala72del) deletion not provided [RCV000056433] Chr12:52949366..52949389 [GRCh38]
Chr12:53343150..53343173 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.418-4C>G single nucleotide variant not provided [RCV000056436] Chr12:52950324 [GRCh38]
Chr12:53344108 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.890C>T (p.Thr297Ile) single nucleotide variant not provided [RCV000056444] Chr12:52951798 [GRCh38]
Chr12:53345582 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.884C>T (p.Thr295Met) single nucleotide variant not provided [RCV000056443] Chr12:52951792 [GRCh38]
Chr12:53345576 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.-15C>T single nucleotide variant not provided [RCV000056430] Chr12:52949159 [GRCh38]
Chr12:53342943 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.307A>G (p.Thr103Ala) single nucleotide variant not provided [RCV000056434] Chr12:52949480 [GRCh38]
Chr12:53343264 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.500+38G>A single nucleotide variant not provided [RCV000056438] Chr12:52950448 [GRCh38]
Chr12:53344232 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.689G>C (p.Ser230Thr) single nucleotide variant not provided [RCV000056439] Chr12:52951512 [GRCh38]
Chr12:53345296 [GRCh37]
Chr12:12q13.13		 likely benign|not provided
GRCh38/hg38 12q13.13(chr12:52851850-53558824)x3 copy number gain See cases [RCV000138030] Chr12:52851850..53558824 [GRCh38]
Chr12:53245634..53952608 [GRCh37]
Chr12:51531901..52238875 [NCBI36]
Chr12:12q13.13		 likely pathogenic
NM_000224.3(KRT18):c.1230C>G (p.Thr410=) single nucleotide variant Hepatitis C virus, susceptibility to [RCV000049576] Chr12:52952779 [GRCh38]
Chr12:53346563 [GRCh37]
Chr12:12q13.13		 not provided
GRCh38/hg38 12q13.12-13.13(chr12:50122359-53248460)x1 copy number loss See cases [RCV000142033] Chr12:50122359..53248460 [GRCh38]
Chr12:50516142..53642244 [GRCh37]
Chr12:48802409..51928511 [NCBI36]
Chr12:12q13.12-13.13		 pathogenic
NM_000224.3(KRT18):c.282C>T (p.Tyr94=) single nucleotide variant Hepatitis C virus, susceptibility to [RCV000049577] Chr12:52949455 [GRCh38]
Chr12:53343239 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.448A>G (p.Ile150Val) single nucleotide variant not provided [RCV000056437] Chr12:52950358 [GRCh38]
Chr12:53344142 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.993C>T (p.Tyr331=) single nucleotide variant not provided [RCV000056445] Chr12:52952163 [GRCh38]
Chr12:53345947 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.782G>A (p.Arg261Gln) single nucleotide variant not provided [RCV000056440] Chr12:52951605 [GRCh38]
Chr12:53345389 [GRCh37]
Chr12:12q13.13		 not provided
NM_000224.3(KRT18):c.822+5G>A single nucleotide variant not provided [RCV000900641] Chr12:52951650 [GRCh38]
Chr12:53345434 [GRCh37]
Chr12:12q13.13		 likely benign
NM_000224.3(KRT18):c.134G>C (p.Arg45Pro) single nucleotide variant Hepatitis C virus, susceptibility to [RCV000049578] Chr12:52949307 [GRCh38]
Chr12:53343091 [GRCh37]
Chr12:12q13.13		 not provided
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
NM_000224.3(KRT18):c.206G>C (p.Gly69Ala) single nucleotide variant Cirrhosis, familial [RCV001331079] Chr12:52949379 [GRCh38]
Chr12:53343163 [GRCh37]
Chr12:12q13.13		 uncertain significance
NM_000224.3(KRT18):c.541G>A (p.Asp181Asn) single nucleotide variant Cirrhosis, familial [RCV001331080] Chr12:52950790 [GRCh38]
Chr12:53344574 [GRCh37]
Chr12:12q13.13		 uncertain significance
NM_000224.3(KRT18):c.356A>G (p.Lys119Arg) single nucleotide variant Inborn genetic diseases [RCV003264426] Chr12:52949529 [GRCh38]
Chr12:53343313 [GRCh37]
Chr12:12q13.13		 uncertain significance
NM_000224.3(KRT18):c.174_175insA (p.Gly59fs) insertion not specified [RCV001733555] Chr12:52949347..52949348 [GRCh38]
Chr12:53343131..53343132 [GRCh37]
Chr12:12q13.13		 benign
NM_000224.3(KRT18):c.557G>A (p.Arg186His) single nucleotide variant Inborn genetic diseases [RCV002906073] Chr12:52950806 [GRCh38]
Chr12:53344590 [GRCh37]
Chr12:12q13.13		 uncertain significance
NM_000224.3(KRT18):c.1277A>C (p.Lys426Thr) single nucleotide variant Inborn genetic diseases [RCV002732605] Chr12:52952826 [GRCh38]
Chr12:53346610 [GRCh37]
Chr12:12q13.13		 uncertain significance
NM_000224.3(KRT18):c.107A>C (p.Tyr36Ser) single nucleotide variant Inborn genetic diseases [RCV002702165] Chr12:52949280 [GRCh38]
Chr12:53343064 [GRCh37]
Chr12:12q13.13		 uncertain significance
NM_000224.3(KRT18):c.989G>A (p.Arg330His) single nucleotide variant Inborn genetic diseases [RCV002763067] Chr12:52952159 [GRCh38]
Chr12:53345943 [GRCh37]
Chr12:12q13.13		 uncertain significance
NM_000224.3(KRT18):c.553C>T (p.Leu185Phe) single nucleotide variant Inborn genetic diseases [RCV002723246] Chr12:52950802 [GRCh38]
Chr12:53344586 [GRCh37]
Chr12:12q13.13		 uncertain significance
NM_000224.3(KRT18):c.1142G>A (p.Arg381His) single nucleotide variant Inborn genetic diseases [RCV003191691] Chr12:52952312 [GRCh38]
Chr12:53346096 [GRCh37]
Chr12:12q13.13		 uncertain significance
NM_000224.3(KRT18):c.910C>G (p.Gln304Glu) single nucleotide variant Inborn genetic diseases [RCV003258388] Chr12:52951818 [GRCh38]
Chr12:53345602 [GRCh37]
Chr12:12q13.13		 uncertain significance
NM_000224.3(KRT18):c.57C>T (p.Val19=) single nucleotide variant not provided [RCV003391852] Chr12:52949230 [GRCh38]
Chr12:53343014 [GRCh37]
Chr12:12q13.13		 likely benign
NM_000224.3(KRT18):c.599A>G (p.Glu200Gly) single nucleotide variant Cirrhosis, familial [RCV003985250] Chr12:52950848 [GRCh38]
Chr12:53344632 [GRCh37]
Chr12:12q13.13		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC106096416 COSMIC
GTEx LOC106096416 GTEx
Human Proteome Map LOC106096416 Human Proteome Map
NCBI Gene LOC106096416 ENTREZGENE