LOC130057352 (ATAC-STARR-seq lymphoblastoid silent region 6574) - Rat Genome Database

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Gene: LOC130057352 (ATAC-STARR-seq lymphoblastoid silent region 6574) Homo sapiens
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Symbol: LOC130057352
Name: ATAC-STARR-seq lymphoblastoid silent region 6574
RGD ID: 329820053
Description: This genomic sequence represents an accessible chromatin region that was validated as a silencer based on its 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) massively parallel reporter assay (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
GRCh381567,066,039 - 67,066,198 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371567,358,377 - 67,358,536 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.01564,887,934 - 64,888,093 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC130057352
38 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_005902.4(SMAD3):c.12C>T (p.Ile4=) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV001117315]|Familial thoracic aortic aneurysm and aortic dissection [RCV001416536] Chr15:67066166 [GRCh38]
Chr15:67358504 [GRCh37]
Chr15:15q22.33		 likely benign|uncertain significance
NM_005902.4(SMAD3):c.6G>A (p.Ser2=) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV001189204] Chr15:67066160 [GRCh38]
Chr15:67358498 [GRCh37]
Chr15:15q22.33		 likely benign
NM_005902.4(SMAD3):c.-28C>T single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV000359576]|Loeys-Dietz syndrome [RCV000318849]|not specified [RCV000128166] Chr15:67066127 [GRCh38]
Chr15:67358465 [GRCh37]
Chr15:15q22.33		 benign
NM_005902.4(SMAD3):c.-15G>A single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV000378447]|Familial thoracic aortic aneurysm and aortic dissection [RCV000288615]|not provided [RCV004714504]|not specified [RCV000128168] Chr15:67066140 [GRCh38]
Chr15:67358478 [GRCh37]
Chr15:15q22.33		 benign
NM_005902.4(SMAD3):c.-1C>T single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV001184772]|not provided [RCV000329392] Chr15:67066154 [GRCh38]
Chr15:67358492 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.-2C>G single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV001185436] Chr15:67066153 [GRCh38]
Chr15:67358491 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.21del (p.Phe7fs) deletion Familial thoracic aortic aneurysm and aortic dissection [RCV001179189] Chr15:67066175 [GRCh38]
Chr15:67358513 [GRCh37]
Chr15:15q22.33		 pathogenic
NM_005902.4(SMAD3):c.23C>G (p.Thr8Ser) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV001948166] Chr15:67066177 [GRCh38]
Chr15:67358515 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.30G>T (p.Pro10=) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV003641011]|Familial thoracic aortic aneurysm and aortic dissection [RCV002325970] Chr15:67066184 [GRCh38]
Chr15:67358522 [GRCh37]
Chr15:15q22.33		 likely benign|conflicting interpretations of pathogenicity
NM_005902.4(SMAD3):c.-38C>T single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV001115860] Chr15:67066117 [GRCh38]
Chr15:67358455 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.36G>A (p.Val12=) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV000774105] Chr15:67066190 [GRCh38]
Chr15:67358528 [GRCh37]
Chr15:15q22.33		 likely benign
NM_005902.4(SMAD3):c.-23C>T single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV000323863]|Loeys-Dietz syndrome [RCV000264993]|not provided [RCV004715738]|not specified [RCV000128167] Chr15:67066132 [GRCh38]
Chr15:67358470 [GRCh37]
Chr15:15q22.33		 benign
NM_005902.4(SMAD3):c.36G>C (p.Val12=) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV003060326] Chr15:67066190 [GRCh38]
Chr15:67358528 [GRCh37]
Chr15:15q22.33		 likely benign
NM_005902.4(SMAD3):c.3G>A (p.Met1Ile) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV001799526]|Familial thoracic aortic aneurysm and aortic dissection [RCV002377898] Chr15:67066157 [GRCh38]
Chr15:67358495 [GRCh37]
Chr15:15q22.33		 pathogenic|likely pathogenic
NM_005902.4(SMAD3):c.5C>A (p.Ser2Ter) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV001218505]|not provided [RCV000521242] Chr15:67066159 [GRCh38]
Chr15:67358497 [GRCh37]
Chr15:15q22.33		 pathogenic|likely pathogenic
NM_005902.4(SMAD3):c.-10C>T single nucleotide variant Ehlers-Danlos syndrome [RCV002276654]|Familial thoracic aortic aneurysm and aortic dissection [RCV001182314] Chr15:67066145 [GRCh38]
Chr15:67358483 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.1A>T (p.Met1Leu) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV001195952]|Familial thoracic aortic aneurysm and aortic dissection [RCV001231422] Chr15:67066155 [GRCh38]
Chr15:67358493 [GRCh37]
Chr15:15q22.33		 pathogenic|likely pathogenic
NM_005902.4(SMAD3):c.15G>A (p.Leu5=) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV002880921] Chr15:67066169 [GRCh38]
Chr15:67358507 [GRCh37]
Chr15:15q22.33		 likely benign
GRCh38/hg38 15q22.2-26.3(chr15:59828460-101920998)x3 copy number gain See cases [RCV000142915] Chr15:59828460..101920998 [GRCh38]
Chr15:60120659..102461201 [GRCh37]
Chr15:57907951..100278724 [NCBI36]
Chr15:15q22.2-26.3		 pathogenic
NC_000015.10:g.(?_66703239)_(67066380_?)del deletion Aortic valve disease 2 [RCV003117503]|Familial thoracic aortic aneurysm and aortic dissection [RCV000708534] Chr15:66703239..67066380 [GRCh38]
Chr15:66995577..67358718 [GRCh37]
Chr15:15q22.31-22.33		 pathogenic|uncertain significance
NM_005902.4(SMAD3):c.17C>T (p.Pro6Leu) single nucleotide variant not provided [RCV000197181] Chr15:67066171 [GRCh38]
Chr15:67358509 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.34G>T (p.Val12Leu) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV000526860] Chr15:67066188 [GRCh38]
Chr15:67358526 [GRCh37]
Chr15:15q22.33		 uncertain significance
NC_000015.10:g.(?_66703239)_(67190556_?)del deletion Familial thoracic aortic aneurysm and aortic dissection [RCV000813979] Chr15:66703239..67190556 [GRCh38]
Chr15:66995577..67482894 [GRCh37]
Chr15:15q22.31-22.33		 pathogenic
NM_005902.4(SMAD3):c.5C>G (p.Ser2Trp) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV003172510] Chr15:67066159 [GRCh38]
Chr15:67358497 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.-115C>T single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV000276717]|Loeys-Dietz syndrome [RCV000299183] Chr15:67066040 [GRCh38]
Chr15:67358378 [GRCh37]
Chr15:15q22.33		 likely benign
NM_005902.4(SMAD3):c.28C>G (p.Pro10Ala) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV004703279] Chr15:67066182 [GRCh38]
Chr15:67358520 [GRCh37]
Chr15:15q22.33		 likely pathogenic|uncertain significance
NM_005902.4(SMAD3):c.1A>C (p.Met1Leu) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV002315227] Chr15:67066155 [GRCh38]
Chr15:67358493 [GRCh37]
Chr15:15q22.33		 pathogenic|likely pathogenic
NM_005902.4(SMAD3):c.30G>A (p.Pro10=) single nucleotide variant not provided [RCV002292900] Chr15:67066184 [GRCh38]
Chr15:67358522 [GRCh37]
Chr15:15q22.33		 likely benign
NM_005902.4(SMAD3):c.-100C>T single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV000354002]|Familial thoracic aortic aneurysm and aortic dissection [RCV000263645] Chr15:67066055 [GRCh38]
Chr15:67358393 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.9C>T (p.Ser3=) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV003999038]|Cardiovascular phenotype [RCV000250533]|Familial thoracic aortic aneurysm and aortic dissection [RCV002518697] Chr15:67066163 [GRCh38]
Chr15:67358501 [GRCh37]
Chr15:15q22.33		 likely benign
NM_005902.4(SMAD3):c.27C>T (p.Pro9=) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV004004129]|Familial thoracic aortic aneurysm and aortic dissection [RCV000654832]|SMAD3-related disorder [RCV004533429] Chr15:67066181 [GRCh38]
Chr15:67358519 [GRCh37]
Chr15:15q22.33		 benign|likely benign
NM_005902.4(SMAD3):c.29dup (p.Ile11fs) duplication Familial thoracic aortic aneurysm and aortic dissection [RCV002435607] Chr15:67066178..67066179 [GRCh38]
Chr15:67358516..67358517 [GRCh37]
Chr15:15q22.33		 pathogenic
NM_005902.4(SMAD3):c.-18C>T single nucleotide variant not specified [RCV000608741] Chr15:67066137 [GRCh38]
Chr15:67358475 [GRCh37]
Chr15:15q22.33		 likely benign
NM_005902.4(SMAD3):c.1A>G (p.Met1Val) single nucleotide variant Aortic aneurysm [RCV001526579] Chr15:67066155 [GRCh38]
Chr15:67358493 [GRCh37]
Chr15:15q22.33		 pathogenic
NM_005902.4(SMAD3):c.-17_-15delinsACA indel Familial thoracic aortic aneurysm and aortic dissection [RCV001526317] Chr15:67066138..67066140 [GRCh38]
Chr15:67358476..67358478 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.33C>T (p.Ile11=) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV004005924]|Familial thoracic aortic aneurysm and aortic dissection [RCV003643481] Chr15:67066187 [GRCh38]
Chr15:67358525 [GRCh37]
Chr15:15q22.33		 likely benign
NM_005902.4(SMAD3):c.41G>C (p.Arg14Pro) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV003876482] Chr15:67066195 [GRCh38]
Chr15:67358533 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.25C>T (p.Pro9Ser) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV004005887]|Familial thoracic aortic aneurysm and aortic dissection [RCV003642766] Chr15:67066179 [GRCh38]
Chr15:67358517 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.11T>C (p.Ile4Thr) single nucleotide variant Familial thoracic aortic aneurysm and aortic dissection [RCV004523813] Chr15:67066165 [GRCh38]
Chr15:67358503 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.-5C>A single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV004013311] Chr15:67066150 [GRCh38]
Chr15:67358488 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.-5del deletion Aneurysm-osteoarthritis syndrome [RCV004013719] Chr15:67066147 [GRCh38]
Chr15:67358485 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.-5C>T single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV004015641] Chr15:67066150 [GRCh38]
Chr15:67358488 [GRCh37]
Chr15:15q22.33		 uncertain significance
NM_005902.4(SMAD3):c.24T>G (p.Thr8=) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV004014248] Chr15:67066178 [GRCh38]
Chr15:67358516 [GRCh37]
Chr15:15q22.33		 likely benign
NM_005902.4(SMAD3):c.2T>C (p.Met1Thr) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV004016898] Chr15:67066156 [GRCh38]
Chr15:67358494 [GRCh37]
Chr15:15q22.33		 likely pathogenic
NM_005902.4(SMAD3):c.13C>T (p.Leu5=) single nucleotide variant Aneurysm-osteoarthritis syndrome [RCV004013257] Chr15:67066167 [GRCh38]
Chr15:67358505 [GRCh37]
Chr15:15q22.33		 likely benign

Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130057352 COSMIC
GTEx LOC130057352 GTEx
Human Proteome Map LOC130057352 Human Proteome Map
NCBI Gene LOC130057352 ENTREZGENE