LOC129936039 (ATAC-STARR-seq lymphoblastoid active region 19337) - Rat Genome Database

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Gene: LOC129936039 (ATAC-STARR-seq lymphoblastoid active region 19337) Homo sapiens
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Symbol: LOC129936039
Name: ATAC-STARR-seq lymphoblastoid active region 19337
RGD ID: 329405278
Description: This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate 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
GRCh3832,921,959 - 2,922,008 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3732,963,643 - 2,963,692 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.032,916,287 - 2,916,336 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:35858748  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p26.3-26.1(chr3:1984526-6852981)x1 copy number loss See cases [RCV000050822] Chr3:1984526..6852981 [GRCh38]
Chr3:2026210..6894668 [GRCh37]
Chr3:2001210..6869668 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-26.1(chr3:32241-5791120)x1 copy number loss See cases [RCV000134257] Chr3:32241..5791120 [GRCh38]
Chr3:73914..5832807 [GRCh37]
Chr3:48914..5807807 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:63843-19510600)x3 copy number gain See cases [RCV000051719] Chr3:63843..19510600 [GRCh38]
Chr3:105526..19552092 [GRCh37]
Chr3:80526..19527096 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:52266-11089569)x1 copy number loss See cases [RCV000051447] Chr3:52266..11089569 [GRCh38]
Chr3:93949..11131255 [GRCh37]
Chr3:68949..11106255 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-26.1(chr3:63843-6977502)x1 copy number loss See cases [RCV000051475] Chr3:63843..6977502 [GRCh38]
Chr3:105526..7019189 [GRCh37]
Chr3:80526..6994189 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:52266-8582037)x1 copy number loss See cases [RCV000051474] Chr3:52266..8582037 [GRCh38]
Chr3:93949..8623723 [GRCh37]
Chr3:68949..8598723 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:63843-9507969)x1 copy number loss See cases [RCV000051476] Chr3:63843..9507969 [GRCh38]
Chr3:105526..9549653 [GRCh37]
Chr3:80526..9524653 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-26.1(chr3:63843-4708786)x1 copy number loss See cases [RCV000051477] Chr3:63843..4708786 [GRCh38]
Chr3:105526..4750470 [GRCh37]
Chr3:80526..4725470 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:63843-8258109)x1 copy number loss See cases [RCV000051478] Chr3:63843..8258109 [GRCh38]
Chr3:105526..8299796 [GRCh37]
Chr3:80526..8274796 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-26.2(chr3:2577647-3615783)x3 copy number gain See cases [RCV000051431] Chr3:2577647..3615783 [GRCh38]
Chr3:2619331..3657467 [GRCh37]
Chr3:2594331..3632467 [NCBI36]
Chr3:3p26.3-26.2		 uncertain significance
GRCh38/hg38 3p26.3-26.1(chr3:52266-5138262)x1 copy number loss See cases [RCV000135586] Chr3:52266..5138262 [GRCh38]
Chr3:93949..5179947 [GRCh37]
Chr3:68949..5154947 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10631310)x1 copy number loss See cases [RCV000143173] Chr3:32241..10631310 [GRCh38]
Chr3:73914..10672995 [GRCh37]
Chr3:48914..10647995 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.2(chr3:2898016-2930391)x1 copy number loss See cases [RCV000137238] Chr3:2898016..2930391 [GRCh38]
Chr3:2939700..2972075 [GRCh37]
Chr3:2914700..2947075 [NCBI36]
Chr3:3p26.2		 benign
GRCh38/hg38 3p26.3-26.1(chr3:52266-6277604)x1 copy number loss See cases [RCV000136675] Chr3:52266..6277604 [GRCh38]
Chr3:93949..6319291 [GRCh37]
Chr3:68949..6294291 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-26.2(chr3:2749924-3037155)x1 copy number loss See cases [RCV000137792] Chr3:2749924..3037155 [GRCh38]
Chr3:2791608..3078839 [GRCh37]
Chr3:2766608..3053839 [NCBI36]
Chr3:3p26.3-26.2		 uncertain significance
GRCh38/hg38 3p26.3-25.2(chr3:32241-12681483)x1 copy number loss See cases [RCV000138143] Chr3:32241..12681483 [GRCh38]
Chr3:73914..12722982 [GRCh37]
Chr3:48914..12697982 [NCBI36]
Chr3:3p26.3-25.2		 pathogenic
GRCh38/hg38 3p26.2-26.1(chr3:2920886-5861108)x1 copy number loss See cases [RCV000136600] Chr3:2920886..5861108 [GRCh38]
Chr3:2962570..5902795 [GRCh37]
Chr3:2937570..5877795 [NCBI36]
Chr3:3p26.2-26.1		 pathogenic
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3 copy number gain See cases [RCV000051097] Chr3:52266..37148076 [GRCh38]
Chr3:93949..37189567 [GRCh37]
Chr3:68949..37164571 [NCBI36]
Chr3:3p26.3-22.2		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:52266-9450310)x1 copy number loss See cases [RCV000137109] Chr3:52266..9450310 [GRCh38]
Chr3:93949..9491994 [GRCh37]
Chr3:68949..9466994 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.1(chr3:32241-13613818)x3 copy number gain See cases [RCV000138946] Chr3:32241..13613818 [GRCh38]
Chr3:73914..13655318 [GRCh37]
Chr3:48914..13630319 [NCBI36]
Chr3:3p26.3-25.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-9469506)x1 copy number loss See cases [RCV000139253] Chr3:32241..9469506 [GRCh38]
Chr3:73914..9511190 [GRCh37]
Chr3:48914..9486190 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:52747-8370373)x1 copy number loss See cases [RCV000139164] Chr3:52747..8370373 [GRCh38]
Chr3:94430..8412059 [GRCh37]
Chr3:69430..8387059 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10323124)x1 copy number loss See cases [RCV000143325] Chr3:32241..10323124 [GRCh38]
Chr3:73914..10364808 [GRCh37]
Chr3:48914..10339808 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3 copy number gain See cases [RCV000138004] Chr3:32241..30064208 [GRCh38]
Chr3:73914..30105699 [GRCh37]
Chr3:48914..30080703 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-9574994)x1 copy number loss See cases [RCV000140239] Chr3:32241..9574994 [GRCh38]
Chr3:73914..9616678 [GRCh37]
Chr3:48914..9591678 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:688897-11051142)x1 copy number loss See cases [RCV000143706] Chr3:688897..11051142 [GRCh38]
Chr3:730581..11092828 [GRCh37]
Chr3:705581..11067828 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-26.2(chr3:2740571-3165943)x3 copy number gain See cases [RCV000143616] Chr3:2740571..3165943 [GRCh38]
Chr3:2782255..3207627 [GRCh37]
Chr3:2757255..3182627 [NCBI36]
Chr3:3p26.3-26.2		 uncertain significance
GRCh38/hg38 3p26.3-26.2(chr3:32241-3355776)x1 copy number loss See cases [RCV000139436] Chr3:32241..3355776 [GRCh38]
Chr3:73914..3397460 [GRCh37]
Chr3:48914..3372460 [NCBI36]
Chr3:3p26.3-26.2		 likely pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:32241-20334387)x3 copy number gain See cases [RCV000137941] Chr3:32241..20334387 [GRCh38]
Chr3:73914..20375879 [GRCh37]
Chr3:48914..20350883 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-26.2(chr3:20213-3244317)x1 copy number loss See cases [RCV000143693] Chr3:20213..3244317 [GRCh38]
Chr3:61891..3286001 [GRCh37]
Chr3:36891..3261001 [NCBI36]
Chr3:3p26.3-26.2		 uncertain significance
GRCh38/hg38 3p26.3-26.2(chr3:2709002-3057632)x1 copy number loss See cases [RCV000142413] Chr3:2709002..3057632 [GRCh38]
Chr3:2750686..3099316 [GRCh37]
Chr3:2725686..3074316 [NCBI36]
Chr3:3p26.3-26.2		 uncertain significance
GRCh38/hg38 3p26.2(chr3:2847667-3320817)x3 copy number gain See cases [RCV000142358] Chr3:2847667..3320817 [GRCh38]
Chr3:2889351..3362501 [GRCh37]
Chr3:2864351..3337501 [NCBI36]
Chr3:3p26.2		 uncertain significance
GRCh38/hg38 3p26.3-26.1(chr3:32241-6065999)x1 copy number loss See cases [RCV000138552] Chr3:32241..6065999 [GRCh38]
Chr3:73914..6107686 [GRCh37]
Chr3:48914..6082686 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3 copy number gain See cases [RCV000141810] Chr3:53308..41381521 [GRCh38]
Chr3:94991..41423012 [GRCh37]
Chr3:69991..41398016 [NCBI36]
Chr3:3p26.3-22.1		 pathogenic
GRCh38/hg38 3p26.2-26.1(chr3:2891585-5911622)x1 copy number loss See cases [RCV000141647] Chr3:2891585..5911622 [GRCh38]
Chr3:2933269..5953309 [GRCh37]
Chr3:2908269..5928309 [NCBI36]
Chr3:3p26.2-26.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-11379835)x1 copy number loss See cases [RCV000138376] Chr3:32241..11379835 [GRCh38]
Chr3:73914..11421309 [GRCh37]
Chr3:48914..11396309 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic|likely benign
GRCh38/hg38 3p26.3-26.2(chr3:2301168-3219257)x1 copy number loss See cases [RCV000053921] Chr3:2301168..3219257 [GRCh38]
Chr3:2342852..3260941 [GRCh37]
Chr3:2317852..3235941 [NCBI36]
Chr3:3p26.3-26.2		 uncertain significance
GRCh38/hg38 3p26.2(chr3:2878363-3006381)x1 copy number loss Delayed speech and language development [RCV000758088] Chr3:2878363..3006381 [GRCh38]
Chr3:3p26.2		 uncertain significance
GRCh38/hg38 3p26.3-26.1(chr3:32241-7056717)x1 copy number loss See cases [RCV000138287] Chr3:32241..7056717 [GRCh38]
Chr3:73914..7098404 [GRCh37]
Chr3:48914..7073404 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-26.2(chr3:2628659-3001914)x3 copy number gain See cases [RCV000138303] Chr3:2628659..3001914 [GRCh38]
Chr3:2670343..3043598 [GRCh37]
Chr3:2645343..3018598 [NCBI36]
Chr3:3p26.3-26.2		 likely benign
GRCh38/hg38 3p26.3-25.3(chr3:20213-11221602)x1 copy number loss See cases [RCV000141731] Chr3:20213..11221602 [GRCh38]
Chr3:61891..11263288 [GRCh37]
Chr3:36891..11238288 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-26.1(chr3:52266-5966084)x3 copy number gain See cases [RCV000142519] Chr3:52266..5966084 [GRCh38]
Chr3:93949..6007771 [GRCh37]
Chr3:68949..5982771 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-8165256)x3 copy number gain See cases [RCV000141319] Chr3:32241..8165256 [GRCh38]
Chr3:73914..8206943 [GRCh37]
Chr3:48914..8181943 [NCBI36]
Chr3:3p26.3-25.3		 likely pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:20213-9362037)x1 copy number loss See cases [RCV000142284] Chr3:20213..9362037 [GRCh38]
Chr3:61891..9403721 [GRCh37]
Chr3:36891..9378721 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-9066287)x1 copy number loss See cases [RCV000140848] Chr3:32241..9066287 [GRCh38]
Chr3:73914..9107971 [GRCh37]
Chr3:48914..9082971 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-26.2(chr3:2644029-3001855)x3 copy number gain See cases [RCV000141396] Chr3:2644029..3001855 [GRCh38]
Chr3:2685713..3043539 [GRCh37]
Chr3:2660713..3018539 [NCBI36]
Chr3:3p26.3-26.2		 uncertain significance
GRCh38/hg38 3p26.3-26.1(chr3:52266-4827490)x1 copy number loss See cases [RCV000142736] Chr3:52266..4827490 [GRCh38]
Chr3:93949..4869174 [GRCh37]
Chr3:68949..4844174 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316345GLUCO224_HGlucose level QTL 224 (human)1.270.008Glucose level3121543441Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129936039 COSMIC
GTEx LOC129936039 GTEx
Human Proteome Map LOC129936039 Human Proteome Map
NCBI Gene LOC129936039 ENTREZGENE