Variant report

Variant	esv33163
Chromosome Location	chr2:56199782-56203845
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFEMP1-1	chr2:56202902-56203042	NONHSAT070812
2	lnc-EFEMP1-1	chr2:56200943-56202732	NONHSAT070812

Extended variants
information (count: 144 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:144 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs187362388	chr2:56199802-56199803	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs72813862	chr2:56199810-56199811	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs112866921	chr2:56199819-56199820	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs543384412	chr2:56199839-56199840	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs532356278	chr2:56199887-56199888	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs552549604	chr2:56199920-56199921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs571281534	chr2:56199941-56199942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs144026416	chr2:56199947-56199948	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs146449781	chr2:56200048-56200049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs548776356	chr2:56200054-56200055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs568703397	chr2:56200075-56200076	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs140845813	chr2:56200076-56200077	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs532054150	chr2:56200094-56200095	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs190609889	chr2:56200135-56200136	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs115464335	chr2:56200145-56200146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs570527443	chr2:56200146-56200147	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs552112982	chr2:56200166-56200167	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs539031006	chr2:56200173-56200174	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs552957013	chr2:56200181-56200182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs573034956	chr2:56200189-56200190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs4453721	chr2:56200190-56200191	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs555133234	chr2:56200265-56200266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs150087732	chr2:56200340-56200341	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs544006536	chr2:56200361-56200362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs4635565	chr2:56200365-56200366	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs544341180	chr2:56200378-56200379	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs4589800	chr2:56200399-56200400	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs181762450	chr2:56200475-56200476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs559724908	chr2:56200487-56200488	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs528779509	chr2:56200495-56200496	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs540959210	chr2:56200549-56200550	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs12472832	chr2:56200573-56200574	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs562260487	chr2:56200624-56200625	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs531078963	chr2:56200682-56200683	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs10192259	chr2:56200747-56200748	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs551036987	chr2:56200801-56200802	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs532318412	chr2:56200870-56200871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs76059728	chr2:56200923-56200924	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs62164513	chr2:56200941-56200942	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs186093815	chr2:56200962-56200963	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs530640770	chr2:56200975-56200976	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs566503407	chr2:56200990-56200991	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs190467389	chr2:56201024-56201025	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs550395870	chr2:56201105-56201106	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs537330886	chr2:56201125-56201126	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs555196537	chr2:56201134-56201135	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs568821344	chr2:56201142-56201143	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs138646108	chr2:56201180-56201181	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs182724114	chr2:56201245-56201246	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs557952730	chr2:56201247-56201248	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:78)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Mental retardation	19951919	CNVD
Myelofibrosis	22110671	CNVD
Microcephaly	20799320	CNVD
camptodactyly	20799320	CNVD
cognitive delay	20799320	CNVD
prenatal and postnatal growth deficiency	20799320	CNVD
ptosis of eyelids	20799320	CNVD
Maculopathy	20981449	CNVD
2p16.1 microdeletion syndrome	22283845	CNVD
Autism	22579565	CNVD
Autism	16963482	CNVD
Autism	21750575	CNVD
idiopathic intellectual disability	16963482	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Multiple myeloma	16616336	CNVD
Follicular lymphoma	17699855	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56193400-56202400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:56194000-56216200	Weak transcription	Pancreas	Pancrea
3	chr2:56195800-56208600	Weak transcription	HUVEC	blood vessel
4	chr2:56198200-56199800	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:56201400-56202200	Enhancers	Stomach Smooth Muscle	stomach
6	chr2:56202200-56203000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:56202200-56203600	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:56202400-56202600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:56202400-56203000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:56202600-56202800	Enhancers	HSMM	muscle
11	chr2:56202600-56203000	Active TSS	GM12878-XiMat	blood
12	chr2:56203000-56203200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:56203000-56204400	Enhancers	Stomach Smooth Muscle	stomach
14	chr2:56203200-56203400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:56203200-56204400	Enhancers	Fetal Stomach	stomach
16	chr2:56203400-56203800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:56203400-56204200	Enhancers	Colon Smooth Muscle	Colon
18	chr2:56203600-56204400	Enhancers	Fetal Muscle Leg	muscle
19	chr2:56203800-56204000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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