Variant report

Variant	esv3400551
Chromosome Location	chr3:140137287-140140035
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMNAT3-9	chr3:140136721-140139968	ucscGeneNc_uc003esv_1

Extended variants
information (count: 176 )
Associated
traits (count: 51 )

Variant overlapped rSNPs/rCNVs (count:176 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs76018905	chr3:140137290-140137291	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs578034559	chr3:140137321-140137322	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs368168635	chr3:140137333-140137334	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs144552784	chr3:140137347-140137348	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs76946774	chr3:140137351-140137352	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs553599048	chr3:140137353-140137354	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs66952275	chr3:140137355-140137356	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs149413803	chr3:140137359-140137360	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs35463586	chr3:140137365-140137366	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs59496482	chr3:140137373-140137374	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs79049037	chr3:140137374-140137375	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs138471523	chr3:140137375-140137376	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs79907113	chr3:140137376-140137377	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs544966536	chr3:140137382-140137383	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs557361769	chr3:140137428-140137429	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs575528978	chr3:140137429-140137430	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs148681968	chr3:140137434-140137435	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs561005375	chr3:140137448-140137449	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs528664637	chr3:140137484-140137485	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs555329690	chr3:140137570-140137571	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs375060596	chr3:140137650-140137651	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs575638537	chr3:140137697-140137698	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs13099443	chr3:140137723-140137724	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs182110314	chr3:140137737-140137738	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs13099601	chr3:140137754-140137755	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs550969200	chr3:140137772-140137773	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs569653539	chr3:140137820-140137821	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs186889849	chr3:140137841-140137842	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs191663874	chr3:140137862-140137863	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs78829180	chr3:140137869-140137870	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs112278003	chr3:140137874-140137875	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs138286232	chr3:140137875-140137876	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs199498335	chr3:140137876-140137877	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs12634537	chr3:140137877-140137878	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs571451366	chr3:140137896-140137897	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs538952919	chr3:140137905-140137906	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs368913613	chr3:140137931-140137932	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs113934058	chr3:140137981-140137982	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs542607826	chr3:140138016-140138017	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs528962514	chr3:140138024-140138025	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs67701000	chr3:140138030-140138031	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs540312271	chr3:140138034-140138035	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs375747533	chr3:140138062-140138063	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs142167385	chr3:140138078-140138079	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs111874234	chr3:140138116-140138117	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs193202674	chr3:140138117-140138118	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs542790502	chr3:140138140-140138141	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs12053843	chr3:140138145-140138146	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs530532062	chr3:140138161-140138162	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs113844745	chr3:140138177-140138178	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:51)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Dyslexia	22102821	CNVD

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140128200-140139600	Weak transcription	Ovary	ovary
2	chr3:140128400-140139600	Weak transcription	Right Atrium	heart
3	chr3:140131400-140139600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:140134800-140139400	Weak transcription	HSMMtube	muscle
5	chr3:140135800-140139800	Weak transcription	Pancreas	Pancrea
6	chr3:140136400-140139400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:140138800-140143600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:140139000-140139200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:140139000-140140200	Enhancers	HUVEC	blood vessel
10	chr3:140139200-140139400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:140139200-140139400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:140139200-140140200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:140139200-140140200	Enhancers	Adipose Nuclei	Adipose
14	chr3:140139200-140141400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:140139200-140144200	Enhancers	HSMM	muscle
16	chr3:140139400-140139600	Enhancers	Brain Substantia Nigra	brain
17	chr3:140139400-140139800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:140139400-140139800	Enhancers	HMEC	breast
19	chr3:140139400-140139800	Enhancers	HSMMtube	muscle
20	chr3:140139400-140139800	Enhancers	NHLF	lung
21	chr3:140139400-140140000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:140139400-140140000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:140139400-140140000	Enhancers	Fetal Stomach	stomach
24	chr3:140139400-140140000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr3:140139400-140140000	Enhancers	NHEK	skin
26	chr3:140139400-140140200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:140139400-140140200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr3:140139400-140140200	Enhancers	Fetal Lung	lung
29	chr3:140139400-140140200	Enhancers	Fetal Muscle Leg	muscle
30	chr3:140139400-140140200	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:140139400-140140200	Enhancers	NH-A	brain
32	chr3:140139400-140140200	Enhancers	Osteobl	bone
33	chr3:140139400-140141000	Enhancers	NHDF-Ad	bronchial
34	chr3:140139400-140144200	Enhancers	Fetal Heart	heart
35	chr3:140139600-140139800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:140139600-140140000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:140139600-140140000	Enhancers	Brain Hippocampus Middle	brain
38	chr3:140139600-140140000	Enhancers	Fetal Muscle Trunk	muscle
39	chr3:140139600-140140000	Enhancers	Right Atrium	heart
40	chr3:140139600-140140200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:140139600-140140200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:140139600-140140200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:140139600-140140200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:140139600-140140200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:140139600-140140200	Enhancers	Placenta	Placenta
46	chr3:140139600-140140200	Enhancers	Gastric	stomach
47	chr3:140139600-140140200	Enhancers	Lung	lung
48	chr3:140139600-140140400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:140139600-140140600	Enhancers	Ovary	ovary
50	chr3:140139800-140140200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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