Variant report

Variant	nsv961318
Chromosome Location	chr2:54818096-54823449
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54785168..54787003-chr2:54819314..54822161,2	K562	blood:
2	chr2:54789266..54791330-chr2:54815899..54818560,2	K562	blood:
3	chr2:54782515..54784267-chr2:54820223..54822640,2	MCF-7	breast:
4	chr2:54815000..54820095-chr2:54820709..54825309,10	K562	blood:
5	chr2:54783987..54787753-chr2:54814113..54820814,10	K562	blood:
6	chr2:54822696..54824811-chr2:54826177..54828033,3	K562	blood:
7	chr2:54818034..54820422-chr2:54821780..54823433,2	MCF-7	breast:
8	chr2:54823186..54826195-chr2:54832588..54835705,3	K562	blood:
9	chr2:54797826..54799514-chr2:54816272..54818809,2	MCF-7	breast:
10	chr2:54818034..54820422-chr2:54821780..54823433,2	MCF-7	breast:
11	chr2:54818759..54820876-chr2:54830874..54833017,2	MCF-7	breast:
12	chr2:54815022..54818519-chr2:54825874..54828742,4	K562	blood:
13	chr2:54816128..54819257-chr2:54823273..54825897,3	MCF-7	breast:
14	chr2:54822318..54824059-chr2:54829758..54831616,2	MCF-7	breast:
15	chr2:54815000..54820095-chr2:54820709..54825309,10	K562	blood:
16	chr2:54815707..54819448-chr2:54820160..54824681,7	K562	blood:
17	chr2:54810337..54813834-chr2:54815762..54818177,4	MCF-7	breast:
18	chr2:54822853..54825212-chr2:54825239..54827897,2	MCF-7	breast:
19	chr2:54806062..54808345-chr2:54823269..54826209,2	MCF-7	breast:
20	chr2:54815707..54819448-chr2:54820160..54824681,7	K562	blood:
21	chr2:54816128..54819257-chr2:54823273..54825897,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115306	chromatin interactions

Extended variants
information (count: 272 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:272 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs183527294	chr2:54818120-54818121	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs74684575	chr2:54818142-54818143	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs372909092	chr2:54818146-54818147	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs538135233	chr2:54818148-54818149	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs142409651	chr2:54818242-54818243	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs138171503	chr2:54818288-54818289	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs113421483	chr2:54818302-54818303	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs577894648	chr2:54818330-54818331	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs374801886	chr2:54818339-54818340	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs540338367	chr2:54818359-54818360	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs539981931	chr2:54818378-54818379	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs559964347	chr2:54818401-54818402	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs188521997	chr2:54818415-54818416	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs560279258	chr2:54818417-54818418	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs542215045	chr2:54818482-54818483	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs369078487	chr2:54818624-54818625	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs142783827	chr2:54818625-54818626	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs531926527	chr2:54818633-54818634	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs551643585	chr2:54818635-54818636	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs79152415	chr2:54818638-54818639	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs139032996	chr2:54818696-54818697	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs542866238	chr2:54818709-54818710	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs191512364	chr2:54818716-54818717	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs369190207	chr2:54818724-54818725	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs562850252	chr2:54818743-54818744	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs75381019	chr2:54818748-54818749	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs376515954	chr2:54818761-54818762	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs536741609	chr2:54818770-54818771	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs550246714	chr2:54818808-54818809	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs183375250	chr2:54818822-54818823	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs538174616	chr2:54818831-54818832	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs186995428	chr2:54818852-54818853	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs531951328	chr2:54818870-54818871	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs7584223	chr2:54818895-54818896	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs375447152	chr2:54818899-54818900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs533702924	chr2:54818913-54818914	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs6545434	chr2:54818921-54818922	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs573693359	chr2:54818969-54818970	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs144810906	chr2:54818973-54818974	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs527767395	chr2:54818977-54818978	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs148635328	chr2:54818992-54818993	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs547930054	chr2:54819034-54819035	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs4374410	chr2:54819088-54819089	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
44	rs545318584	chr2:54819134-54819135	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs200015362	chr2:54819141-54819142	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs191433805	chr2:54819167-54819168	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs527899501	chr2:54819345-54819346	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs77625263	chr2:54819352-54819353	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs76147120	chr2:54819360-54819361	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs72920521	chr2:54819401-54819402	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:77)

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
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	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
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:439 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54802200-54822600	Weak transcription	Esophagus	oesophagus
2	chr2:54804000-54822400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:54805600-54819800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:54807000-54826000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:54807200-54819800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:54807800-54818800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:54808800-54822800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:54809400-54821600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:54809600-54825800	Weak transcription	Brain Germinal Matrix	brain
11	chr2:54811400-54819400	Enhancers	Stomach Mucosa	stomach
12	chr2:54811600-54818400	Enhancers	Brain Substantia Nigra	brain
13	chr2:54811600-54819200	Enhancers	Fetal Heart	heart
14	chr2:54811800-54818800	Enhancers	Brain Hippocampus Middle	brain
15	chr2:54814000-54822800	Weak transcription	Ovary	ovary
16	chr2:54814200-54818200	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr2:54814200-54819600	Weak transcription	Fetal Stomach	stomach
18	chr2:54814400-54819800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr2:54814600-54818600	Enhancers	Small Intestine	intestine
20	chr2:54814600-54819400	Enhancers	Fetal Brain Male	brain
21	chr2:54814800-54818400	Enhancers	Fetal Intestine Large	intestine
22	chr2:54814800-54819600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:54814800-54819800	Weak transcription	HSMMtube	muscle
24	chr2:54814800-54820000	Enhancers	Primary B cells from peripheral blood	blood
25	chr2:54815000-54818200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:54815000-54818400	Enhancers	Thymus	Thymus
27	chr2:54815000-54819000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:54815000-54819200	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr2:54815000-54819800	Weak transcription	Fetal Brain Female	brain
30	chr2:54815400-54818200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:54815400-54823400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:54816000-54820400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:54816400-54818200	Flanking Active TSS	Liver	Liver
35	chr2:54816600-54818200	Enhancers	Adipose Nuclei	Adipose
36	chr2:54816600-54819000	Enhancers	Fetal Intestine Small	intestine
37	chr2:54816600-54819200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:54816600-54819200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:54816600-54822400	Weak transcription	Gastric	stomach
40	chr2:54816600-54822400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:54816600-54822600	Weak transcription	Colonic Mucosa	Colon
42	chr2:54816600-54828400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:54816800-54819800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr2:54816800-54819800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:54816800-54819800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:54816800-54819800	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:54816800-54819800	Enhancers	Fetal Thymus	thymus
48	chr2:54816800-54820000	Weak transcription	HSMM	muscle
49	chr2:54816800-54820800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:54816800-54821200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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