Variant report

Variant	esv3450421
Chromosome Location	chr3:17788701-17789124
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	ATF2	chr3:17788877-17789581	GM12878	blood:	n/a	n/a
2	ATF2	chr3:17788846-17789498	GM12878	blood:	n/a	n/a
3	BATF	chr3:17788981-17789714	GM12878	blood:	n/a	n/a
4	BATF	chr3:17789048-17789497	GM12878	blood:	n/a	n/a
5	BCL11A	chr3:17789078-17789499	GM12878	blood:	n/a	n/a
6	BCL3	chr3:17789028-17789478	GM12878	blood:	n/a	n/a
7	BCLAF1	chr3:17788789-17789579	GM12878	blood:	n/a	n/a
8	BHLHE40	chr3:17788631-17789474	GM12878	blood:	n/a	n/a
9	BHLHE40	chr3:17788726-17789033	K562	blood:	n/a	n/a
10	CBX3	chr3:17788461-17789056	K562	blood:	n/a	n/a
11	CEBPB	chr3:17788872-17788873	K562	blood:	n/a	n/a
12	CEBPB	chr3:17788887-17789632	GM12878	blood:	n/a	n/a
13	CEBPB	chr3:17789120-17789324	GM12878	blood:	n/a	n/a
14	CHD2	chr3:17788665-17789443	GM12878	blood:	n/a	n/a
15	CTCF	chr3:17788980-17789130	GM12872	blood:	n/a	n/a
16	CTCF	chr3:17788940-17789090	GM12873	blood:	n/a	n/a
17	CTCF	chr3:17788683-17788734	GM19239	blood:	n/a	n/a
18	CUX1	chr3:17788800-17789382	GM12878	blood:	n/a	n/a
19	CUX1	chr3:17788809-17789026	K562	blood:	n/a	n/a
20	EBF1	chr3:17788842-17789423	GM12878	blood:	n/a	n/a
21	EBF1	chr3:17788593-17789119	GM12878	blood:	n/a	n/a
22	EBF1	chr3:17788637-17789490	GM12878	blood:	n/a	n/a
23	EGR1	chr3:17788767-17788994	K562	blood:	n/a	n/a
24	EGR1	chr3:17788745-17789039	K562	blood:	n/a	n/a
25	ELK1	chr3:17789050-17789434	GM12878	blood:	n/a	n/a
26	EP300	chr3:17788922-17789485	GM12878	blood:	n/a	chr3:17789293-17789302 chr3:17789189-17789198 chr3:17789216-17789230
27	EP300	chr3:17788687-17789435	GM12878	blood:	n/a	chr3:17789293-17789302 chr3:17789189-17789198 chr3:17789216-17789230
28	EP300	chr3:17788630-17789542	GM12878	blood:	n/a	chr3:17789293-17789302 chr3:17789189-17789198 chr3:17789216-17789230
29	ETS1	chr3:17789006-17789460	GM12878	blood:	n/a	n/a
30	FOXM1	chr3:17788939-17789570	GM12878	blood:	n/a	n/a
31	FOXM1	chr3:17788923-17789616	GM12878	blood:	n/a	n/a
32	HEY1	chr3:17788844-17789124	HepG2	liver:	n/a	n/a
33	HNF4A	chr3:17788709-17789205	HepG2	liver:	n/a	chr3:17788804-17788819
34	HNF4A	chr3:17788956-17789295	HepG2	liver:	n/a	n/a
35	HNF4G	chr3:17788619-17789235	HepG2	liver:	n/a	n/a
36	IKZF1	chr3:17788672-17789621	GM12878	blood:	n/a	n/a
37	IRF4	chr3:17788883-17789580	GM12878	blood:	n/a	n/a
38	IRF4	chr3:17788963-17789582	GM12878	blood:	n/a	n/a
39	MAFF	chr3:17788547-17788808	HepG2	liver:	n/a	n/a
40	MAZ	chr3:17788831-17788875	GM12878	blood:	n/a	n/a
41	MEF2A	chr3:17789042-17789603	GM12878	blood:	n/a	n/a
42	MEF2A	chr3:17789021-17789558	GM12878	blood:	n/a	n/a
43	MEF2C	chr3:17789035-17789453	GM12878	blood:	n/a	n/a
44	MTA3	chr3:17788511-17789739	GM12878	blood:	n/a	n/a
45	MTA3	chr3:17788954-17789512	GM12878	blood:	n/a	n/a
46	MXI1	chr3:17788931-17789447	GM12878	blood:	n/a	n/a
47	NFATC1	chr3:17789036-17789500	GM12878	blood:	n/a	n/a
48	NFATC1	chr3:17788799-17789459	GM12878	blood:	n/a	n/a
49	NFIC	chr3:17788773-17789605	GM12878	blood:	n/a	n/a
50	NFIC	chr3:17788912-17789591	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:17782115..17785920-chr3:17786903..17792058,8	MCF-7	breast:
2	chr3:17787258..17788942-chr3:17794142..17796862,2	MCF-7	breast:

Variant related genes	Relation type
TBC1D5	TF binding region
ENSG00000131374	chromatin interactions

Extended variants
information (count: 14 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs145450276	chr3:17788707-17788708	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs541220961	chr3:17788775-17788776	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs564422004	chr3:17788810-17788811	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs192756386	chr3:17788813-17788814	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs4908970	chr3:17788866-17788867	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs560070639	chr3:17788891-17788892	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs11927769	chr3:17788902-17788903	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs182597957	chr3:17788913-17788914	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs548753371	chr3:17788979-17788980	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs11916424	chr3:17788989-17788990	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs534167733	chr3:17789003-17789004	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs547581699	chr3:17789028-17789029	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs4908971	chr3:17789074-17789075	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs550800515	chr3:17789124-17789125	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:69)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
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
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
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	21364760	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17784800-17788800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:17784800-17790600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:17784800-17790800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:17784800-17790800	Weak transcription	Gastric	stomach
5	chr3:17784800-17794000	Weak transcription	Pancreas	Pancrea
6	chr3:17785000-17788800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:17785000-17789000	Weak transcription	Primary T cells from cord blood	blood
8	chr3:17785000-17790600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:17785000-17790600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:17785000-17794000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:17785200-17788800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:17785200-17788800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr3:17785200-17788800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:17785200-17788800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:17785200-17789000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:17785200-17789000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:17785200-17790600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:17785200-17790600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:17785200-17790600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:17785200-17790800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:17785400-17788800	Weak transcription	Fetal Thymus	thymus
22	chr3:17785400-17789000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:17785400-17790600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:17785400-17790600	Weak transcription	HMEC	breast
25	chr3:17785400-17790800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:17785400-17790800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:17785400-17790800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:17785400-17790800	Weak transcription	NHEK	skin
29	chr3:17785400-17791000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:17785600-17788800	Weak transcription	Fetal Intestine Small	intestine
31	chr3:17785600-17790800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:17785600-17790800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:17785600-17790800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:17785800-17788800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:17785800-17788800	Enhancers	HepG2	liver
36	chr3:17785800-17789000	Weak transcription	Dnd41	blood
37	chr3:17785800-17790800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:17785800-17790800	Weak transcription	A549	lung
39	chr3:17786400-17789600	Enhancers	K562	blood
40	chr3:17787000-17790800	Weak transcription	Liver	Liver
41	chr3:17787200-17791000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:17788400-17789000	Enhancers	Small Intestine	intestine
43	chr3:17788400-17789200	Flanking Active TSS	GM12878-XiMat	blood
44	chr3:17788400-17789400	Enhancers	HSMM	muscle
45	chr3:17788400-17789800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr3:17788400-17789800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:17788400-17790200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr3:17788400-17791800	Enhancers	Primary B cells from peripheral blood	blood
49	chr3:17788400-17792800	Enhancers	Primary B cells from cord blood	blood
50	chr3:17788600-17789000	Flanking Active TSS	Duodenum Mucosa	Duodenum

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