Variant report

Variant	nsv999198
Chromosome Location	chr3:88410579-88491242
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	BACH1	chr3:88434387-88434629	H1-hESC	embryonic stem cell:	n/a	n/a
2	BACH1	chr3:88438892-88438979	K562	blood:	n/a	n/a
3	CEBPB	chr3:88434165-88434583	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr3:88427165-88427365	H1-hESC	embryonic stem cell:	n/a	chr3:88427292-88427305
5	CTCF	chr3:88428358-88428558	GM12878	blood:	n/a	chr3:88428421-88428434 chr3:88428419-88428437 chr3:88428414-88428435
6	CTCF	chr3:88449307-88449344	GM20000	blood:	n/a	n/a
7	CTCF	chr3:88468481-88468493	GM13976	blood:	n/a	n/a
8	CTCF	chr3:88428380-88428530	GM12865	blood:	n/a	chr3:88428421-88428434 chr3:88428419-88428437 chr3:88428414-88428435
9	CTCF	chr3:88463612-88463648	GM20000	blood:	n/a	n/a
10	CTCF	chr3:88428300-88428450	MCF-7	breast:	n/a	chr3:88428421-88428434 chr3:88428419-88428437 chr3:88428414-88428435
11	CTCF	chr3:88412093-88412153	MCF-7	breast:	n/a	n/a
12	CUX1	chr3:88482645-88483002	GM12878	blood:	n/a	n/a
13	E2F4	chr3:88412425-88412431	MCF10A-Er-Src	breast:	n/a	n/a
14	E2F4	chr3:88434209-88434418	MCF10A-Er-Src	breast:	n/a	n/a
15	E2F4	chr3:88485218-88485410	MCF10A-Er-Src	breast:	n/a	n/a
16	E2F4	chr3:88428630-88428740	MCF10A-Er-Src	breast:	n/a	n/a
17	E2F4	chr3:88418524-88418809	MCF10A-Er-Src	breast:	n/a	n/a
18	E2F4	chr3:88473166-88473219	MCF10A-Er-Src	breast:	n/a	n/a
19	EBF1	chr3:88482668-88483329	GM12878	blood:	n/a	chr3:88482873-88482882 chr3:88482872-88482882 chr3:88482872-88482883
20	EBF1	chr3:88482670-88483081	GM12878	blood:	n/a	chr3:88482873-88482882 chr3:88482872-88482882 chr3:88482872-88482883
21	EBF1	chr3:88482660-88483080	GM12878	blood:	n/a	chr3:88482873-88482882 chr3:88482872-88482882 chr3:88482872-88482883
22	EP300	chr3:88482788-88483105	GM12878	blood:	n/a	n/a
23	FAM48A	chr3:88483023-88483046	GM12878	blood:	n/a	n/a
24	FAM48A	chr3:88420642-88420679	GM12878	blood:	n/a	n/a
25	FAM48A	chr3:88489851-88489922	GM12878	blood:	n/a	n/a
26	FOS	chr3:88434160-88434546	MCF10A-Er-Src	breast:	n/a	n/a
27	FOS	chr3:88478226-88478560	MCF10A-Er-Src	breast:	n/a	chr3:88478343-88478350
28	FOS	chr3:88478283-88478616	MCF10A-Er-Src	breast:	n/a	chr3:88478343-88478350
29	FOS	chr3:88418507-88418873	MCF10A-Er-Src	breast:	n/a	chr3:88418682-88418690 chr3:88418682-88418690 chr3:88418682-88418689 chr3:88418681-88418691
30	FOS	chr3:88434282-88434422	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr3:88483740-88483838	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr3:88483619-88483847	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr3:88469831-88470068	MCF10A-Er-Src	breast:	n/a	chr3:88469988-88469997
34	FOS	chr3:88418513-88418849	MCF10A-Er-Src	breast:	n/a	chr3:88418682-88418690 chr3:88418682-88418690 chr3:88418682-88418689 chr3:88418681-88418691
35	FOS	chr3:88469911-88470140	MCF10A-Er-Src	breast:	n/a	chr3:88469988-88469997
36	FOS	chr3:88414893-88415009	MCF10A-Er-Src	breast:	n/a	n/a
37	FOS	chr3:88434153-88434620	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr3:88418495-88418849	MCF10A-Er-Src	breast:	n/a	chr3:88418682-88418690 chr3:88418682-88418690 chr3:88418682-88418689 chr3:88418681-88418691
39	FOS	chr3:88418502-88418854	MCF10A-Er-Src	breast:	n/a	chr3:88418682-88418690 chr3:88418682-88418690 chr3:88418682-88418689 chr3:88418681-88418691
40	FOS	chr3:88434218-88434619	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr3:88429317-88429680	HUVEC	blood vessel:	n/a	n/a
42	FOS	chr3:88469277-88469534	MCF10A-Er-Src	breast:	n/a	n/a
43	FOSL2	chr3:88411581-88411969	MCF-7	breast:	n/a	n/a
44	FOXA1	chr3:88411651-88411881	HepG2	liver:	n/a	n/a
45	FOXA1	chr3:88411550-88411886	HepG2	liver:	n/a	n/a
46	FOXA2	chr3:88411679-88411926	HepG2	liver:	n/a	n/a
47	FOXM1	chr3:88482652-88483139	GM12878	blood:	n/a	n/a
48	FOXM1	chr3:88489828-88490259	GM12878	blood:	n/a	n/a
49	GATA3	chr3:88445804-88446004	SH-SY5Y	brain:	n/a	n/a
50	GATA3	chr3:88411542-88411957	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:7969749..7970528-chr3:88470088..88470821,2	MCF-7	breast:
2	chr3:88443258..88445795-chr3:88448224..88450369,2	K562	blood:
3	chr3:88443258..88445795-chr3:88448224..88450369,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf38-2	chr3:88474992-88475125	l_2409_chr3:88470262-88514628_testes
2	lnc-C3orf38-2	chr3:88431734-88431938	NONHSAT090703
3	lnc-C3orf38-2	chr3:88418571-88418634	XLOC_002727
4	lnc-C3orf38-2	chr3:88431735-88431938	XLOC_002727
5	lnc-C3orf38-2	chr3:88431735-88431938	XLOC_002727
6	lnc-C3orf38-2	chr3:88470263-88470483	l_2409_chr3:88470262-88514628_testes

Variant related genes	Relation type
ENSG00000207316	TF binding region
ECE1	miRNA target sites
HCCS	miRNA target sites

Extended variants
information (count: 1171 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:1171 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs549537092	chr3:88411228-88411229	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs543468993	chr3:88411282-88411283	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs567711364	chr3:88411300-88411301	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs535408962	chr3:88411325-88411326	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs114772510	chr3:88411352-88411353	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs565549857	chr3:88411407-88411408	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs556807087	chr3:88411449-88411450	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs146517645	chr3:88411464-88411465	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs559033445	chr3:88411478-88411479	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs1114268	chr3:88411491-88411492	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs530087669	chr3:88411529-88411530	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs189734829	chr3:88411554-88411555	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs1080301	chr3:88411665-88411666	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs140908838	chr3:88411686-88411687	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs375276394	chr3:88411688-88411689	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs556323416	chr3:88411704-88411705	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs574883526	chr3:88411705-88411706	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs542541925	chr3:88411709-88411710	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs34789963	chr3:88411754-88411755	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs369342019	chr3:88411767-88411768	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs182858071	chr3:88411783-88411784	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs372846958	chr3:88411811-88411812	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs572691929	chr3:88411831-88411832	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs576968159	chr3:88411853-88411854	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs546050092	chr3:88411862-88411863	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs541601197	chr3:88411867-88411868	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs531337883	chr3:88411902-88411903	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs549846888	chr3:88411950-88411951	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs559733635	chr3:88411961-88411962	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs199857844	chr3:88411962-88411963	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs547306511	chr3:88411986-88411987	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs1080302	chr3:88412005-88412006	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs539099420	chr3:88412008-88412009	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs533235457	chr3:88412040-88412041	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs34403133	chr3:88412062-88412063	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs551321054	chr3:88412074-88412075	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs57731162	chr3:88412101-88412102	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs368431567	chr3:88412147-88412148	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs150085785	chr3:88412184-88412185	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs556648356	chr3:88412187-88412188	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs9812498	chr3:88412199-88412200	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs116066601	chr3:88418007-88418008	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs542530430	chr3:88418023-88418024	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs570787343	chr3:88418030-88418031	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs572551323	chr3:88418053-88418054	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs545587888	chr3:88418059-88418060	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs564172362	chr3:88418064-88418065	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs189582584	chr3:88418072-88418073	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs543050368	chr3:88418098-88418099	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs561339242	chr3:88418149-88418150	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
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
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Wilms tumour	21544195	CNVD
Soft tissue tumor	16732325	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Non-small cell lung cancer	21829676	CNVD
Lung cancer	19547694	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88411200-88411800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:88411400-88412200	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr3:88411600-88411800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:88418000-88419200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:88428200-88428600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:88433600-88434400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:88434000-88434400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr3:88434000-88434400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:88434000-88434400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:88434000-88434600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:88447600-88448000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:88448600-88449000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr3:88448600-88449600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:88449000-88449400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr3:88452400-88452800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:88452800-88457800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:88453800-88455000	Enhancers	Primary T cells from cord blood	blood
18	chr3:88454600-88454800	Enhancers	Fetal Heart	heart
19	chr3:88454800-88455400	Weak transcription	Fetal Heart	heart
20	chr3:88455000-88457200	Weak transcription	Primary T cells from cord blood	blood
21	chr3:88455400-88456200	Enhancers	Fetal Heart	heart
22	chr3:88456000-88456800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr3:88457200-88459200	Enhancers	Primary T cells from cord blood	blood
24	chr3:88457800-88458600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:88457800-88459400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:88458000-88458200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:88458200-88458400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr3:88459000-88460000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:88459000-88460000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:88459200-88459600	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr3:88459200-88460200	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:88459600-88460000	Active TSS	Primary T cells from cord blood	blood
33	chr3:88459800-88460200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:88460000-88460800	Enhancers	Primary T cells from cord blood	blood
35	chr3:88460800-88461200	Weak transcription	Primary T cells from cord blood	blood
36	chr3:88461200-88461600	Enhancers	Primary T cells from cord blood	blood
37	chr3:88461400-88461800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:88467400-88467800	Enhancers	Fetal Brain Male	brain
39	chr3:88476600-88482000	Weak transcription	Primary B cells from cord blood	blood
40	chr3:88482000-88482600	Enhancers	Primary B cells from cord blood	blood
41	chr3:88482600-88483000	Enhancers	GM12878-XiMat	blood
42	chr3:88482600-88483400	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr3:88482600-88483600	Enhancers	Dnd41	blood
44	chr3:88482800-88483200	Enhancers	Fetal Muscle Leg	muscle
45	chr3:88482800-88483800	Active TSS	NHDF-Ad	bronchial
46	chr3:88482800-88484800	Enhancers	Primary B cells from peripheral blood	blood
47	chr3:88483000-88483600	Flanking Active TSS	GM12878-XiMat	blood
48	chr3:88483400-88483800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:88483400-88485600	Enhancers	Primary B cells from cord blood	blood
50	chr3:88483600-88484000	Flanking Active TSS	Dnd41	blood

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