Variant report

Variant	esv3334579
Chromosome Location	chr3:48734845-48735306
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	CTCF	chr3:48735260-48735410	GM06990	blood:	n/a	n/a
2	POLR2A	chr3:48735299-48735318	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:48735175-48735181	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:48735266-48735744	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:48735216-48735303	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:48735150-48735796	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:48735279-48735902	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr3:48735088-48735335	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr3:48734881-48735012	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:48735288-48735507	K562	blood:	n/a	n/a
11	POLR2A	chr3:48734837-48734849	K562	blood:	n/a	n/a
12	POLR2A	chr3:48735304-48736033	GM12891	blood:	n/a	n/a
13	POLR2A	chr3:48734963-48735966	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48732542..48735376-chr3:48750993..48752883,2	K562	blood:
2	chr3:48725665..48728051-chr3:48734995..48736912,2	MCF-7	breast:

Variant related genes	Relation type
IP6K2	TF binding region
ENSG00000068745	chromatin interactions

Extended variants
information (count: 19 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs184058780	chr3:48734851-48734852	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs80026423	chr3:48734861-48734862	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs35746542	chr3:48734921-48734922	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs57818116	chr3:48734922-48734923	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs397766672	chr3:48734945-48734946	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs28520903	chr3:48734946-48734947	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs71324915	chr3:48734947-48734948	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs28475500	chr3:48734948-48734949	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs71324916	chr3:48734958-48734959	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs555180834	chr3:48734962-48734963	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs549910352	chr3:48735001-48735002	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs576320912	chr3:48735006-48735007	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs543753260	chr3:48735074-48735075	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs34462230	chr3:48735092-48735093	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs35941761	chr3:48735121-48735122	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs565239557	chr3:48735151-48735152	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs6442129	chr3:48735256-48735257	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs541037326	chr3:48735269-48735270	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs547087248	chr3:48735297-48735298	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:100)

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	21987784	CNVD

Chromatin state (count:139 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
2	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
3	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
4	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
5	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
6	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:48724800-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:48724800-48737600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:48724800-48738400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:48725000-48738600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:48725000-48738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:48725000-48740800	Strong transcription	Dnd41	blood
14	chr3:48725200-48738600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:48731200-48735000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:48732200-48735200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:48732400-48736400	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr3:48732800-48735400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:48732800-48744800	Weak transcription	Small Intestine	intestine
21	chr3:48732800-48745400	Weak transcription	Psoas Muscle	Psoas
22	chr3:48733000-48735600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:48733000-48736200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:48733000-48736400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:48733000-48740200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:48733000-48744800	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:48733000-48745400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
29	chr3:48733200-48735200	Weak transcription	Placenta	Placenta
30	chr3:48733200-48735400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:48733200-48735400	Weak transcription	Lung	lung
32	chr3:48733200-48735400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:48733200-48735400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:48733200-48735600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:48733200-48736000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:48733200-48736200	Weak transcription	Adipose Nuclei	Adipose
37	chr3:48733200-48736200	Weak transcription	Spleen	Spleen
38	chr3:48733200-48736800	Weak transcription	Colonic Mucosa	Colon
39	chr3:48733200-48737600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr3:48733200-48738600	Strong transcription	Fetal Lung	lung
41	chr3:48733200-48738800	Strong transcription	Fetal Muscle Leg	muscle
42	chr3:48733200-48740800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr3:48733200-48744000	Weak transcription	Esophagus	oesophagus
44	chr3:48733200-48746000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:48733200-48746000	Strong transcription	Fetal Intestine Small	intestine
46	chr3:48733200-48746200	Weak transcription	Right Ventricle	heart
47	chr3:48733600-48735800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:48733600-48735800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:48733600-48739200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:48733800-48735400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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