Variant report

Variant	esv3459580
Chromosome Location	chr2:56338448-56341124
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:56315975..56318654-chr2:56340489..56342924,2	K562	blood:
2	chr2:56337806..56341873-chr2:56342839..56347033,7	K562	blood:
3	chr2:56337806..56342628-chr2:56343291..56347033,6	K562	blood:
4	chr2:56336331..56339032-chr2:56340759..56342871,3	K562	blood:
5	chr2:56338244..56341178-chr2:56349675..56352414,2	MCF-7	breast:
6	chr2:56336331..56339032-chr2:56340759..56342871,3	K562	blood:

Variant related genes	Relation type
ENSG00000229805	chromatin interactions

Extended variants
information (count: 92 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:92 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs545173958	chr2:56338480-56338481	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs564749474	chr2:56338532-56338533	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs6545543	chr2:56338546-56338547	Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
4	rs572438360	chr2:56338566-56338567	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs367600497	chr2:56338576-56338577	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs190432590	chr2:56338628-56338629	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs7558709	chr2:56338660-56338661	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs13420560	chr2:56338713-56338714	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs550462589	chr2:56338765-56338766	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs563896507	chr2:56338768-56338769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs532694409	chr2:56338811-56338812	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs551997717	chr2:56338821-56338822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs151013751	chr2:56338869-56338870	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs140365912	chr2:56338919-56338920	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs369626153	chr2:56338922-56338923	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs549693650	chr2:56338981-56338982	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs199790029	chr2:56338993-56338994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs534395281	chr2:56339010-56339011	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs182675609	chr2:56339043-56339044	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs187007747	chr2:56339044-56339045	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs117668293	chr2:56339045-56339046	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs556790440	chr2:56339079-56339080	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs368714702	chr2:56339101-56339102	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs373349562	chr2:56339117-56339118	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs570321744	chr2:56339131-56339132	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs77742331	chr2:56339136-56339137	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs552888612	chr2:56339144-56339145	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs149740258	chr2:56339213-56339214	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs541150597	chr2:56339292-56339293	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs555020070	chr2:56339294-56339295	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs574859022	chr2:56339330-56339331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs191241822	chr2:56339341-56339342	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs563933387	chr2:56339384-56339385	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs115531945	chr2:56339404-56339405	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs145584527	chr2:56339428-56339429	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs116824635	chr2:56339440-56339441	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs182615150	chr2:56339462-56339463	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs141327694	chr2:56339541-56339542	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs567719627	chr2:56339548-56339549	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs113962764	chr2:56339560-56339561	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs530383709	chr2:56339567-56339568	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs375513365	chr2:56339628-56339629	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs147074554	chr2:56339655-56339656	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs147681488	chr2:56339663-56339664	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs371564196	chr2:56339681-56339682	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs142347577	chr2:56339697-56339698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs10179694	chr2:56339722-56339723	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs535145803	chr2:56339734-56339735	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs555055031	chr2:56339768-56339769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs535186869	chr2:56339781-56339782	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

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
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56336400-56344000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:56336600-56340600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:56337200-56340400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:56339400-56339600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:56339800-56347000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:56340000-56340200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:56340200-56340600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:56340400-56340800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:56340400-56341200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:56340400-56341200	Enhancers	Fetal Kidney	kidney
11	chr2:56340400-56341200	Enhancers	Fetal Stomach	stomach
12	chr2:56340600-56341000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr2:56340600-56341200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr2:56340600-56341400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:56340600-56344800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:56340800-56341000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:56340800-56341200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr2:56340800-56341400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:56341000-56341400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:56341000-56344000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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