Variant report

Variant	nsv521030
Chromosome Location	chr2:47249239-47255059
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:22)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:57919156..57921575-chr2:47249552..47252093,2	MCF-7	breast:
2	chr2:47246499..47248286-chr2:47253507..47255645,2	MCF-7	breast:
3	chr2:47251517..47253255-chr2:47403256..47405239,2	K562	blood:
4	chr2:47252397..47254046-chr2:47254810..47257644,2	K562	blood:
5	chr2:47248098..47250499-chr2:47402045..47403673,2	K562	blood:
6	chr2:47247505..47249498-chr2:47258978..47261043,2	K562	blood:
7	chr2:47242011..47245119-chr2:47248786..47251159,3	K562	blood:
8	chr2:47247292..47249498-chr2:47258978..47261257,2	K562	blood:
9	chr2:47227819..47229844-chr2:47253559..47255515,2	K562	blood:
10	chr2:47249673..47251618-chr2:47253667..47255571,2	MCF-7	breast:
11	chr2:47239533..47242401-chr2:47254885..47256539,3	MCF-7	breast:
12	chr2:47250659..47252384-chr2:47268724..47270646,2	MCF-7	breast:
13	chr2:47252454..47254562-chr2:47258233..47260100,2	K562	blood:
14	chr2:47252113..47260352-chr2:47399089..47405669,11	MCF-7	breast:
15	chr2:47253562..47255469-chr2:47401214..47402778,2	K562	blood:
16	chr2:47246848..47250170-chr2:47255935..47259327,3	MCF-7	breast:
17	chr2:47252232..47263251-chr2:47397787..47406051,20	MCF-7	breast:
18	chr2:47252397..47254046-chr2:47254810..47257644,2	K562	blood:
19	chr2:47247796..47250364-chr2:47260163..47262120,2	MCF-7	breast:
20	chr2:47249673..47251618-chr2:47253667..47255571,2	MCF-7	breast:
21	chr2:47247534..47249636-chr2:47250357..47252583,2	MCF-7	breast:
22	chr2:47247534..47249636-chr2:47250357..47252583,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALM2-6	chr2:47253068-47253374	expReg_chr2_3630_-
2	lnc-CALM2-5	chr2:47253515-47254279	expReg_chr2_3631_-

No data

Variant related genes	Relation type
ENSG00000068724	chromatin interactions
ENSG00000143933	chromatin interactions

Extended variants
information (count: 352 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:352 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3814036	chr2:47249239-47249240	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs566131080	chr2:47249242-47249243	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs536952621	chr2:47249268-47249269	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs78914469	chr2:47249271-47249272	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs573697346	chr2:47249274-47249275	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs187190299	chr2:47249275-47249276	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs555865935	chr2:47249279-47249280	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs10209037	chr2:47249294-47249295	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs3814037	chr2:47249295-47249296	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs560306240	chr2:47249300-47249301	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs572099292	chr2:47249334-47249335	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs34170116	chr2:47249339-47249340	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs542534905	chr2:47249351-47249352	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs560815271	chr2:47249356-47249357	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs531486677	chr2:47249418-47249419	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs549790322	chr2:47249422-47249423	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs565131125	chr2:47249444-47249445	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs532678061	chr2:47249522-47249523	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs76556164	chr2:47249552-47249553	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs566263516	chr2:47249559-47249560	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs536811197	chr2:47249573-47249574	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs548786967	chr2:47249577-47249578	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs114742796	chr2:47249580-47249581	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs191600873	chr2:47249606-47249607	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs556165366	chr2:47249625-47249626	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs182320925	chr2:47249626-47249627	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs201116175	chr2:47249657-47249658	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs113926474	chr2:47249675-47249676	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs186710547	chr2:47249687-47249688	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs538730772	chr2:47249689-47249690	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs13430717	chr2:47249712-47249713	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs571675837	chr2:47249727-47249728	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs577262154	chr2:47249742-47249743	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs192621416	chr2:47249779-47249780	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs546179422	chr2:47249800-47249801	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs185570552	chr2:47249806-47249807	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs542447148	chr2:47249811-47249812	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs11695048	chr2:47249816-47249817	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs575975843	chr2:47249821-47249822	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs190478678	chr2:47249831-47249832	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs13405102	chr2:47249832-47249833	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs532353920	chr2:47249839-47249840	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs547888722	chr2:47249864-47249865	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs540839097	chr2:47249905-47249906	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs139042487	chr2:47249946-47249947	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs17036119	chr2:47249966-47249967	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs570256016	chr2:47249976-47249977	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs149875391	chr2:47249985-47249986	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs147965861	chr2:47249986-47249987	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs571244100	chr2:47250023-47250024	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Breast cancer	17603634	CNVD
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
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Bladder cancer	21909424	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
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Non-small cell lung cancer	18927303	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Myelofibrosis	22110671	CNVD
Hypotonia	17579669	CNVD
Hypotonia-Cystinuria syndrome	16385448	CNVD
Glioblastoma multiforme	17002787	CNVD
Cystinuria	17625506	CNVD
Breast cancer	16272173	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Lung cancer	17297452	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Ovarian cancer	22355333	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:320 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47213600-47256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:47214000-47262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:47222000-47260600	Weak transcription	Small Intestine	intestine
4	chr2:47230200-47302800	Strong transcription	Dnd41	blood
5	chr2:47232000-47265000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:47232400-47257000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:47234400-47283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:47236000-47278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:47236600-47253600	Strong transcription	Fetal Intestine Small	intestine
10	chr2:47236600-47259200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:47236600-47259200	Weak transcription	Fetal Kidney	kidney
12	chr2:47236800-47251600	Weak transcription	Fetal Lung	lung
13	chr2:47237000-47254200	Weak transcription	Ovary	ovary
14	chr2:47237000-47260400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:47238200-47253400	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr2:47238200-47253600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr2:47238200-47253800	Strong transcription	HepG2	liver
18	chr2:47240000-47249800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:47240200-47251800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:47240200-47256000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:47240800-47251400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:47241400-47250400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:47242200-47250400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:47242200-47253400	Weak transcription	HMEC	breast
25	chr2:47243800-47249800	Weak transcription	Hela-S3	cervix
26	chr2:47243800-47260200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:47243800-47260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:47243800-47260800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:47243800-47261000	Weak transcription	K562	blood
30	chr2:47244000-47249400	Weak transcription	NH-A	brain
31	chr2:47244000-47250600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:47244000-47252800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:47244000-47253200	Weak transcription	Stomach Mucosa	stomach
34	chr2:47244000-47254200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:47244000-47256000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:47244000-47256800	Strong transcription	Osteobl	bone
37	chr2:47244000-47257200	Weak transcription	HUVEC	blood vessel
38	chr2:47244000-47258800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr2:47244000-47260600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:47244200-47261200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:47244400-47257000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:47244600-47257000	Strong transcription	NHLF	lung
43	chr2:47244600-47258800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr2:47244800-47256200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:47244800-47256800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:47244800-47258800	Strong transcription	Placenta	Placenta
47	chr2:47245000-47255600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:47245800-47251800	Strong transcription	GM12878-XiMat	blood
49	chr2:47245800-47253000	Strong transcription	A549	lung
50	chr2:47245800-47254400	Strong transcription	Lung	lung

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