Variant report

Variant	nsv967015
Chromosome Location	chr3:48370774-48381957
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr3:48375096-48375362	GM12878	blood:	n/a	n/a
2	CEBPB	chr3:48375520-48375578	K562	blood:	n/a	chr3:48375532-48375543
3	CEBPB	chr3:48375502-48375543	HepG2	liver:	n/a	chr3:48375532-48375543
4	CTCF	chr3:48374979-48374994	GM19240	blood:	n/a	n/a
5	CTCF	chr3:48374980-48375130	GM12873	blood:	n/a	n/a
6	CTCF	chr3:48374880-48375030	GM12864	blood:	n/a	n/a
7	CTCF	chr3:48374983-48375051	Fibrobl	skin:	n/a	n/a
8	CTCF	chr3:48372089-48372190	Lung_OC	lung:	n/a	n/a
9	CTCF	chr3:48374996-48375029	GM19240	blood:	n/a	n/a
10	EGR1	chr3:48374855-48375056	K562	blood:	n/a	n/a
11	EP300	chr3:48373595-48373822	T-47D	breast:	n/a	n/a
12	FOS	chr3:48379085-48379297	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr3:48379183-48379211	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr3:48379066-48379341	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr3:48379098-48379294	MCF10A-Er-Src	breast:	n/a	n/a
16	FOXA1	chr3:48380247-48380451	T-47D	breast:	n/a	n/a
17	FOXA1	chr3:48380193-48380451	T-47D	breast:	n/a	n/a
18	GABPA	chr3:48376819-48377242	HL-60	blood:	n/a	n/a
19	GATA3	chr3:48373535-48373885	T-47D	breast:	n/a	n/a
20	GATA3	chr3:48373368-48373891	MCF-7	breast:	n/a	n/a
21	GATA3	chr3:48370541-48370777	T-47D	breast:	n/a	n/a
22	HA-E2F1	chr3:48373218-48373676	MCF-7	breast:	n/a	n/a
23	JUND	chr3:48380573-48380576	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr3:48376727-48377219	NB4	blood:	n/a	n/a
25	MYC	chr3:48376825-48377104	NB4	blood:	n/a	n/a
26	POLR2A	chr3:48376830-48377228	HL-60	blood:	n/a	n/a
27	POLR2A	chr3:48380265-48380309	MCF-7	breast:	n/a	n/a
28	POLR2A	chr3:48376774-48377202	HL-60	blood:	n/a	n/a
29	POU2F2	chr3:48374800-48375339	GM12891	blood:	n/a	chr3:48375325-48375339
30	POU2F2	chr3:48375057-48375430	GM12878	blood:	n/a	chr3:48375325-48375339
31	SPI1	chr3:48376887-48377237	HL-60	blood:	n/a	n/a
32	SPI1	chr3:48376524-48376859	GM12891	blood:	n/a	n/a
33	SPI1	chr3:48380057-48380582	HL-60	blood:	n/a	n/a
34	SPI1	chr3:48370633-48371010	HL-60	blood:	n/a	n/a
35	TCF7L2	chr3:48373597-48373898	MCF-7	breast:	n/a	n/a
36	YY1	chr3:48377153-48377333	K562	blood:	n/a	n/a
37	YY1	chr3:48377057-48377422	H1-hESC	embryonic stem cell:	n/a	n/a
38	ZNF217	chr3:48373632-48373835	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48341856..48344117-chr3:48376394..48379085,2	MCF-7	breast:

Variant related genes	Relation type
SPINK8	TF binding region
ENSG00000172113	chromatin interactions

Extended variants
information (count: 398 )
Associated
traits (count: 99 )

Variant overlapped rSNPs/rCNVs (count:398 , 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	rs544631425	chr3:48370823-48370824	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs189924606	chr3:48370862-48370863	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs550447505	chr3:48370875-48370876	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs571650841	chr3:48370907-48370908	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs35708314	chr3:48370911-48370912	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs542352176	chr3:48371022-48371023	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs181111355	chr3:48371028-48371029	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs562203563	chr3:48371077-48371078	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs535949118	chr3:48371085-48371086	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs138214395	chr3:48371092-48371093	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs373266224	chr3:48371195-48371196	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs186130675	chr3:48371322-48371323	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs571259811	chr3:48371359-48371360	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs207463142	chr3:48371389-48371390	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs190949496	chr3:48371583-48371584	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs143066183	chr3:48371601-48371602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs543290597	chr3:48371669-48371670	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs180835551	chr3:48371671-48371672	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs111549036	chr3:48371685-48371686	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs145141749	chr3:48371697-48371698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs374940864	chr3:48371783-48371784	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs545392358	chr3:48371788-48371789	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs560494167	chr3:48371795-48371796	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs527745651	chr3:48371806-48371807	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs374921386	chr3:48371866-48371867	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs543110378	chr3:48371876-48371877	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs561273565	chr3:48371880-48371881	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs531924986	chr3:48371923-48371924	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs141507627	chr3:48371932-48371933	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs571588704	chr3:48371964-48371965	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs532691836	chr3:48371965-48371966	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs546957837	chr3:48371966-48371967	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs565337602	chr3:48371995-48371996	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs535912337	chr3:48372048-48372049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs186383018	chr3:48372117-48372118	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs569683557	chr3:48372120-48372121	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs537227093	chr3:48372131-48372132	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs558808090	chr3:48372196-48372197	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs9759097	chr3:48372206-48372207	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs577174991	chr3:48372271-48372272	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs9825637	chr3:48372282-48372283	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs554162634	chr3:48372290-48372291	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs575771060	chr3:48372315-48372316	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs373523957	chr3:48372326-48372327	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs572470031	chr3:48372373-48372374	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs190831801	chr3:48372418-48372419	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs59313008	chr3:48372437-48372438	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs564339599	chr3:48372449-48372450	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs13082158	chr3:48372470-48372471	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs543969919	chr3:48372505-48372506	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:99)

Disease	PMID	Source
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
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
small cell lung cancer	20016488	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
Kartagener syndrome	16639409	CNVD
Biliary cancer	19435499	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
Acute myeloid leukemia	17268525	CNVD
Salivary gland tumor	18059337	CNVD
Gastric cancer	16891809	CNVD
Night blindness	17160897	CNVD
Cancer	17160897	CNVD
Breast cancer	20409316	CNVD
Lung cancer	17297452	CNVD
Multiple myeloma	16616336	CNVD
Effusion lymphoma	18079361	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Melanoma	17363583	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medullary thyroid carcinoma	18765511	CNVD
abnormal development	18461090	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48363000-48373400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr3:48370200-48370800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:48370600-48371400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:48370800-48371400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:48371400-48373200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:48371400-48373600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:48372200-48377600	Enhancers	Placenta	Placenta
8	chr3:48372800-48374600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:48373200-48374000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:48373400-48374000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr3:48373600-48374400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr3:48373600-48374600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr3:48373800-48374000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:48374000-48376200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:48374000-48377400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr3:48374400-48375000	Enhancers	Primary hematopoietic stem cells	blood
17	chr3:48374400-48375400	Active TSS	Primary B cells from cord blood	blood
18	chr3:48374400-48375800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:48374400-48375800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr3:48374400-48377600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:48374600-48375000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr3:48375000-48375600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr3:48375000-48376600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:48375400-48377800	Enhancers	Primary B cells from cord blood	blood
25	chr3:48375600-48376400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:48375800-48376200	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr3:48375800-48376800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:48376200-48377400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr3:48376200-48377800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr3:48376400-48376600	Enhancers	Primary hematopoietic stem cells	blood
31	chr3:48376600-48377200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr3:48376600-48380000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:48376800-48377200	Active TSS	Adipose Nuclei	Adipose
34	chr3:48376800-48377600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:48377200-48377800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:48377400-48377800	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:48377400-48380800	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr3:48377600-48379600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:48377600-48379600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:48377600-48387800	Weak transcription	Placenta	Placenta
41	chr3:48377800-48378800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr3:48377800-48379600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:48378400-48378600	Enhancers	Esophagus	oesophagus
44	chr3:48378600-48379000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:48378600-48379600	Weak transcription	Esophagus	oesophagus
46	chr3:48378600-48381000	Enhancers	HSMM	muscle
47	chr3:48378800-48379000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr3:48379000-48379400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:48379000-48379600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:48379200-48380000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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