Variant report

Variant	nsv590438
Chromosome Location	chr3:61547707-61549659
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:234744695..234746368-chr3:61546699..61548508,2	MCF-7	breast:
2	chr3:61547884..61549685-chr3:61773585..61775750,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPRG-2	chr3:61547525-61548046	NONHSAT090170

Variant related genes	Relation type
ENSG00000168264	chromatin interactions

Extended variants
information (count: 109 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:109 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs188240370	chr3:61547739-61547740	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs540050184	chr3:61547744-61547745	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs565019581	chr3:61547773-61547774	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs532062626	chr3:61547795-61547796	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs550227278	chr3:61547811-61547812	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs562166525	chr3:61547845-61547846	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs180692943	chr3:61547853-61547854	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs370243100	chr3:61547907-61547908	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs369507033	chr3:61547911-61547912	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs371238609	chr3:61547912-61547913	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs373215703	chr3:61547924-61547925	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs376402081	chr3:61547925-61547926	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs200942304	chr3:61547926-61547927	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs534430030	chr3:61547931-61547932	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs369741118	chr3:61547932-61547933	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs199608216	chr3:61547939-61547940	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs373513928	chr3:61547947-61547948	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs77802872	chr3:61548001-61548002	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs375586923	chr3:61548009-61548010	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs140017853	chr3:61548010-61548011	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs556669186	chr3:61548012-61548013	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs149847925	chr3:61548018-61548019	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs146419543	chr3:61548022-61548023	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs142428806	chr3:61548039-61548040	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs2365955	chr3:61548046-61548047	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs201903648	chr3:61548052-61548053	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs375806986	chr3:61548060-61548061	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs201006177	chr3:61548090-61548091	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs573053022	chr3:61548134-61548135	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs540462953	chr3:61548179-61548180	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs558481773	chr3:61548182-61548183	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs576583531	chr3:61548183-61548184	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs543923775	chr3:61548188-61548189	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs562209257	chr3:61548190-61548191	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs377577172	chr3:61548215-61548216	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs529673668	chr3:61548220-61548221	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs146855048	chr3:61548226-61548227	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs541437997	chr3:61548253-61548254	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs371076875	chr3:61548257-61548258	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs13094820	chr3:61548270-61548271	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs560885828	chr3:61548273-61548274	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs6445224	chr3:61548285-61548286	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs552792287	chr3:61548290-61548291	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs368163413	chr3:61548301-61548302	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs531909133	chr3:61548373-61548374	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs550334264	chr3:61548401-61548402	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs370726755	chr3:61548460-61548461	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs111694959	chr3:61548462-61548463	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs187186518	chr3:61548463-61548464	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs72888649	chr3:61548502-61548503	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Acute myeloid leukemia	20729466	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
small cell lung cancer	20016488	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	19490591	CNVD
Autism	18414403	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-small cell lung cancer	20864512	CNVD
Metastatic melanoma	17975146	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Breast cancer	21509527	CNVD
Myelofibrosis	22110671	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Urothelial cell carcinoma	18451213	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Colorectal cancer	16272173	CNVD
Mental retardation	17847001	CNVD
Neuroticism	17667963	CNVD
Squamous cell cancer	19047905	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Autism	22102821	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Cancer	20164919	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:264 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61545000-61547800	Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr3:61545000-61549600	Active TSS	NHEK	skin
3	chr3:61545000-61550800	Active TSS	Psoas Muscle	Psoas
4	chr3:61545200-61549400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:61545400-61549000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:61545400-61549600	Active TSS	Duodenum Mucosa	Duodenum
7	chr3:61545400-61550400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr3:61545400-61550800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:61545400-61550800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:61545400-61550800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:61545600-61547800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr3:61545600-61548200	Active TSS	Fetal Brain Female	brain
13	chr3:61545600-61548400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:61545600-61548400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:61545600-61548400	Active TSS	Fetal Muscle Trunk	muscle
16	chr3:61545600-61548400	Active TSS	Placenta	Placenta
17	chr3:61545600-61548400	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr3:61545600-61549000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:61545600-61549000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:61545600-61549000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:61545600-61549000	Active TSS	Liver	Liver
22	chr3:61545600-61549200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:61545600-61549200	Active TSS	Fetal Lung	lung
24	chr3:61545600-61549400	Active TSS	H1 Cell Line	embryonic stem cell
25	chr3:61545600-61549400	Active TSS	Brain Angular Gyrus	brain
26	chr3:61545600-61549400	Active TSS	Fetal Brain Male	brain
27	chr3:61545600-61549600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:61545600-61549600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr3:61545600-61549800	Active TSS	HSMM	muscle
30	chr3:61545600-61550200	Active TSS	NHLF	lung
31	chr3:61545600-61550600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:61545600-61550600	Active TSS	Colon Smooth Muscle	Colon
33	chr3:61545600-61550600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr3:61545600-61550600	Active TSS	NHDF-Ad	bronchial
35	chr3:61545600-61550800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr3:61545600-61550800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:61545600-61550800	Active TSS	Fetal Kidney	kidney
38	chr3:61545600-61550800	Active TSS	Left Ventricle	heart
39	chr3:61545600-61550800	Active TSS	HSMMtube	muscle
40	chr3:61545600-61551000	Active TSS	Aorta	Aorta
41	chr3:61545800-61547800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:61545800-61548000	Active TSS	Fetal Stomach	stomach
43	chr3:61545800-61548200	Active TSS	Brain Germinal Matrix	brain
44	chr3:61545800-61548400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:61545800-61548400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:61545800-61548400	Active TSS	Fetal Intestine Large	intestine
47	chr3:61545800-61549000	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr3:61545800-61549000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:61545800-61549000	Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:61545800-61549000	Active TSS	Colonic Mucosa	Colon

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