Variant report

Variant	esv3411417
Chromosome Location	chr3:48598988-48599337
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	chr3:48598875-48599182	GM12878	blood:	n/a	chr3:48599007-48599018 chr3:48599008-48599018
2	BHLHE40	chr3:48598951-48599084	K562	blood:	n/a	n/a
3	BHLHE40	chr3:48598979-48599065	GM12878	blood:	n/a	n/a
4	CBX3	chr3:48598776-48599053	K562	blood:	n/a	n/a
5	CTCF	chr3:48598920-48599070	HMF	breast:	n/a	n/a
6	FOS	chr3:48598973-48599175	MCF10A-Er-Src	breast:	n/a	chr3:48599011-48599018 chr3:48599009-48599020
7	FOS	chr3:48598870-48599147	HUVEC	blood vessel:	n/a	chr3:48599011-48599018 chr3:48599009-48599020
8	FOS	chr3:48598892-48599147	MCF10A-Er-Src	breast:	n/a	chr3:48599011-48599018 chr3:48599009-48599020
9	FOS	chr3:48598878-48599127	MCF10A-Er-Src	breast:	n/a	chr3:48599011-48599018 chr3:48599009-48599020
10	FOS	chr3:48598917-48599117	MCF10A-Er-Src	breast:	n/a	chr3:48599011-48599018 chr3:48599009-48599020
11	FOSL1	chr3:48598808-48599196	K562	blood:	n/a	chr3:48599011-48599018
12	FOSL2	chr3:48598498-48599237	HepG2	liver:	n/a	chr3:48598654-48598663 chr3:48599010-48599021 chr3:48599011-48599018
13	FOSL2	chr3:48598742-48599249	A549	lung:	n/a	chr3:48599010-48599021 chr3:48599011-48599018
14	FOSL2	chr3:48598791-48599171	HepG2	liver:	n/a	chr3:48599010-48599021 chr3:48599011-48599018
15	HEY1	chr3:48598344-48599005	HepG2	liver:	n/a	chr3:48598427-48598436
16	IRF4	chr3:48598809-48599252	GM12878	blood:	n/a	n/a
17	JUND	chr3:48598437-48599185	K562	blood:	n/a	chr3:48598654-48598663 chr3:48599011-48599018 chr3:48599009-48599020
18	JUND	chr3:48598397-48599345	SK-N-SH	brain:	n/a	chr3:48598654-48598663 chr3:48599011-48599018 chr3:48599009-48599020
19	JUND	chr3:48598917-48599650	A549	lung:	n/a	chr3:48599011-48599018 chr3:48599009-48599020
20	JUND	chr3:48598834-48599165	HepG2	liver:	n/a	chr3:48599011-48599018 chr3:48599009-48599020
21	MAX	chr3:48598772-48599153	SK-N-SH	brain:	n/a	n/a
22	MAX	chr3:48597494-48599126	NB4	blood:	n/a	chr3:48598678-48598688
23	MAX	chr3:48598849-48599131	K562	blood:	n/a	n/a
24	MAZ	chr3:48598194-48599001	K562	blood:	n/a	chr3:48598678-48598688
25	MAZ	chr3:48597740-48599146	IMR90	lung:	n/a	chr3:48598678-48598688
26	MXI1	chr3:48598000-48599272	IMR90	lung:	n/a	n/a
27	MXI1	chr3:48598471-48599054	HepG2	liver:	n/a	n/a
28	MXI1	chr3:48593292-48599174	SK-N-SH	brain:	n/a	n/a
29	MYC	chr3:48598140-48599096	NB4	blood:	n/a	chr3:48598678-48598688
30	MYC	chr3:48598978-48599032	K562	blood:	n/a	n/a
31	MYC	chr3:48598978-48599070	MCF-7	breast:	n/a	n/a
32	PBX3	chr3:48599209-48599819	A549	lung:	n/a	n/a
33	POLR2A	chr3:48597367-48601913	U87	brain:	n/a	n/a
34	POLR2A	chr3:48598540-48600602	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr3:48588992-48602017	U87	brain:	n/a	n/a
36	POLR2A	chr3:48597305-48601913	U87	brain:	n/a	n/a
37	POLR2A	chr3:48595475-48603087	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:48599262-48599661	A549	lung:	n/a	n/a
39	POLR2A	chr3:48598401-48599179	Gliobla	brain:	n/a	n/a
40	POLR2A	chr3:48598956-48599112	A549	lung:	n/a	n/a
41	POLR2A	chr3:48595520-48602478	A549	lung:	n/a	n/a
42	POLR2A	chr3:48599272-48599489	A549	lung:	n/a	n/a
43	POLR2A	chr3:48597192-48599116	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:48598945-48599236	A549	lung:	n/a	n/a
45	POLR2A	chr3:48599264-48599671	A549	lung:	n/a	n/a
46	POLR2A	chr3:48598911-48599224	A549	lung:	n/a	n/a
47	POLR2A	chr3:48599246-48599684	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr3:48592306-48602182	U87	brain:	n/a	n/a
49	POLR2A	chr3:48598902-48599111	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr3:48598839-48599797	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48598382..48600078-chr3:48601801..48604759,2	K562	blood:
2	chr3:48598893..48601513-chr3:48603815..48606240,3	MCF-7	breast:
3	chr3:48595568..48597473-chr3:48598401..48600580,2	MCF-7	breast:
4	chr3:48592800..48598084-chr3:48598125..48603493,9	MCF-7	breast:
5	chr3:48598407..48599969-chr3:48607969..48610789,2	K562	blood:
6	chr3:48592861..48595715-chr3:48598424..48603731,6	K562	blood:

Variant related genes	Relation type
PFKFB4	TF binding region
ENSG00000114268	chromatin interactions
ENSG00000114270	chromatin interactions

Extended variants
information (count: 12 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs529559534	chr3:48599015-48599016	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs373517262	chr3:48599032-48599033	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs373751197	chr3:48599100-48599101	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs533235631	chr3:48599106-48599107	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs568789368	chr3:48599117-48599118	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs71074261	chr3:48599131-48599132	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs373675834	chr3:48599149-48599150	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs557879359	chr3:48599173-48599174	Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs1079134	chr3:48599222-48599223	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs533895309	chr3:48599224-48599225	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs117583613	chr3:48599323-48599324	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs573764324	chr3:48599330-48599331	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:102)

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
Non-syndromic sensorineural hearing loss	18451855	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:163 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48593600-48599000	Enhancers	Stomach Mucosa	stomach
2	chr3:48594600-48599200	Enhancers	Fetal Heart	heart
3	chr3:48594600-48599200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr3:48595000-48599200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:48595200-48599000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:48595200-48599000	Enhancers	Fetal Thymus	thymus
7	chr3:48595400-48602000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:48595800-48599000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr3:48595800-48599000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:48595800-48599000	Flanking Active TSS	HepG2	liver
11	chr3:48595800-48599200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:48596200-48599000	Enhancers	Primary B cells from cord blood	blood
13	chr3:48596400-48600000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:48596400-48600200	Enhancers	Spleen	Spleen
15	chr3:48596400-48603200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:48596600-48606800	Genic enhancers	A549	lung
17	chr3:48596600-48626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:48596800-48599000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:48597000-48599000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr3:48597200-48599000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:48597200-48599000	Strong transcription	NHEK	skin
22	chr3:48597200-48599400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:48597200-48599800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:48597200-48600200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:48597400-48599000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr3:48597400-48599000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr3:48597400-48599000	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr3:48597400-48599200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:48597400-48599200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:48597400-48599200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:48597400-48599200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr3:48597600-48599000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:48597600-48599000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr3:48597600-48599000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:48597600-48599000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:48597600-48599000	Enhancers	Gastric	stomach
37	chr3:48597600-48599000	Flanking Active TSS	Osteobl	bone
38	chr3:48597600-48599200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:48597600-48599400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:48597600-48599800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr3:48597600-48606200	Genic enhancers	HMEC	breast
42	chr3:48597800-48599000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr3:48597800-48599000	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr3:48597800-48599000	Enhancers	Fetal Intestine Small	intestine
45	chr3:48597800-48599000	Flanking Active TSS	HSMM	muscle
46	chr3:48597800-48599000	Enhancers	HUVEC	blood vessel
47	chr3:48597800-48599200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:48597800-48599400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr3:48598000-48599000	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr3:48598000-48599000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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