Variant report

Variant	esv3339879
Chromosome Location	chr3:53713646-53714124
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	chr3:53708590..53712002-chr3:53712853..53715298,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL17RB-1	chr3:53713021-53713790	NONHSAT090004

Extended variants
information (count: 18 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs544717640	chr3:53713649-53713650	Weak transcription Enhancers Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs146376157	chr3:53713651-53713652	Weak transcription Enhancers Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs562697276	chr3:53713652-53713653	Weak transcription Enhancers Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs532016698	chr3:53713654-53713655	Weak transcription Enhancers Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs551747782	chr3:53713690-53713691	Weak transcription Enhancers Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs735652	chr3:53713721-53713722	Weak transcription Enhancers Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs548465750	chr3:53713745-53713746	Weak transcription Enhancers Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs528325971	chr3:53713794-53713795	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs375269375	chr3:53713809-53713810	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs746487	chr3:53713854-53713855	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs527257718	chr3:53713894-53713895	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs568126001	chr3:53713926-53713927	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs537564300	chr3:53713980-53713981	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs551123421	chr3:53714020-53714021	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs570940961	chr3:53714037-53714038	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs1380610	chr3:53714038-53714039	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs113815874	chr3:53714048-53714049	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs553046304	chr3:53714101-53714102	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:93)

Disease	PMID	Source
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	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
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	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 peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Ventriculomegaly	21325761	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Lung cancer	16618734	CNVD
Neuroblastoma	19686582	CNVD
Renal cell carcinoma	18765545	CNVD
Adrenocortical carcinoma	18281524	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Breast cancer	21509527	CNVD

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:53698000-53714000	Weak transcription	Brain Substantia Nigra	brain
3	chr3:53709000-53714000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53709400-53713800	Weak transcription	Fetal Brain Male	brain
5	chr3:53710200-53714000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:53711200-53714000	Weak transcription	Fetal Kidney	kidney
7	chr3:53711600-53713800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:53711800-53713800	Weak transcription	Fetal Heart	heart
9	chr3:53711800-53714000	Weak transcription	Left Ventricle	heart
10	chr3:53711800-53714000	Weak transcription	Right Atrium	heart
11	chr3:53713200-53716000	Strong transcription	Fetal Intestine Large	intestine
12	chr3:53713600-53714400	Enhancers	Fetal Stomach	stomach
13	chr3:53713600-53714600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:53713600-53714600	Enhancers	Fetal Brain Female	brain
15	chr3:53713600-53714600	Enhancers	Fetal Lung	lung
16	chr3:53713600-53715000	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr3:53713800-53714000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:53713800-53714000	Enhancers	Stomach Smooth Muscle	stomach
19	chr3:53713800-53714200	Flanking Active TSS	Fetal Brain Male	brain
20	chr3:53713800-53714600	Enhancers	Colon Smooth Muscle	Colon
21	chr3:53713800-53714600	Enhancers	Fetal Muscle Leg	muscle
22	chr3:53713800-53714600	Enhancers	Psoas Muscle	Psoas
23	chr3:53713800-53715800	Strong transcription	Fetal Intestine Small	intestine
24	chr3:53713800-53717600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:53714000-53714200	Enhancers	Fetal Heart	heart
26	chr3:53714000-53714200	Enhancers	Fetal Kidney	kidney
27	chr3:53714000-53714200	Enhancers	Lung	lung
28	chr3:53714000-53714400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:53714000-53714400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:53714000-53714400	Active TSS	Stomach Smooth Muscle	stomach
31	chr3:53714000-53714600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:53714000-53714600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
33	chr3:53714000-53714600	Enhancers	Brain Cingulate Gyrus	brain
34	chr3:53714000-53714600	Enhancers	Brain Substantia Nigra	brain
35	chr3:53714000-53714600	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr3:53714000-53714600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr3:53714000-53714600	Enhancers	Left Ventricle	heart
38	chr3:53714000-53714600	Enhancers	Right Atrium	heart
39	chr3:53714000-53714600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:53714000-53715400	Enhancers	Brain Angular Gyrus	brain

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