Variant report

Variant	esv3461088
Chromosome Location	chr3:48957723-48958853
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr3:48958070-48958148	K562	blood:	n/a	n/a
2	CHD1	chr3:48955533-48957765	IMR90	lung:	n/a	n/a
3	HEY1	chr3:48957868-48958141	K562	blood:	n/a	n/a
4	MAX	chr3:48955477-48957761	HepG2	liver:	n/a	chr3:48957381-48957391
5	MAX	chr3:48955518-48957729	HCT-116	colon:	n/a	chr3:48957381-48957391
6	MXI1	chr3:48955445-48957924	SK-N-SH	brain:	n/a	n/a
7	NR2F2	chr3:48955881-48957781	K562	blood:	n/a	chr3:48956651-48956666
8	POLR2A	chr3:48958839-48959326	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:48958815-48959239	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:48955395-48957740	GM12878	blood:	n/a	n/a
11	ZNF384	chr3:48955642-48958084	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48722838..48724823-chr3:48955919..48958463,2	K562	blood:
2	chr3:48956190..48958160-chr3:48963848..48966266,2	MCF-7	breast:
3	chr3:48955694..48958185-chr3:49021057..49023573,2	K562	blood:
4	chr3:48882526..48886164-chr3:48952991..48958735,8	K562	blood:
5	chr3:48752504..48754863-chr3:48957920..48960085,2	K562	blood:
6	chr3:48777544..48781186-chr3:48954650..48958375,5	K562	blood:
7	chr3:48954616..48957728-chr3:49043769..49045935,3	K562	blood:
8	chr3:48956178..48958930-chr3:48964681..48967359,2	MCF-7	breast:
9	chr3:48831351..48833653-chr3:48957027..48958695,2	MCF-7	breast:
10	chr3:48955974..48957797-chr3:49448912..49450941,2	K562	blood:
11	chr3:48956092..48958804-chr3:49057398..49059224,2	K562	blood:
12	chr3:48700863..48702620-chr3:48955867..48958209,2	K562	blood:
13	chr3:48933374..48937590-chr3:48954193..48958596,7	K562	blood:
14	chr3:48954426..48959569-chr3:49057203..49060067,5	K562	blood:
15	chr3:48882526..48887589-chr3:48952932..48958567,11	K562	blood:

No data

Variant related genes	Relation type
ARIH2OS	TF binding region
ARIH2	TF binding region
ENSG00000228350	chromatin interactions
ENSG00000145022	chromatin interactions
ENSG00000114302	chromatin interactions
ENSG00000207605	chromatin interactions
ENSG00000178149	chromatin interactions
ENSG00000224424	chromatin interactions
ENSG00000067560	chromatin interactions
ENSG00000178057	chromatin interactions
ENSG00000068745	chromatin interactions
ENSG00000213672	chromatin interactions
ENSG00000235236	chromatin interactions
ENSG00000178252	chromatin interactions
ENSG00000178537	chromatin interactions
ENSG00000199032	chromatin interactions
ENSG00000177479	chromatin interactions
ENSG00000273211	chromatin interactions

Extended variants
information (count: 30 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs542262232	chr3:48957723-48957724	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	18 gene(s)	Overlapped CNVs	n/a
2	rs9637481	chr3:48957814-48957815	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs113356851	chr3:48957843-48957844	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
4	rs563708938	chr3:48957862-48957863	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
5	rs11706805	chr3:48957907-48957908	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
6	rs13064272	chr3:48957917-48957918	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
7	rs546087134	chr3:48958023-48958024	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
8	rs13068948	chr3:48958030-48958031	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
9	rs113359009	chr3:48958038-48958039	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
10	rs530906492	chr3:48958073-48958074	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
11	rs79115177	chr3:48958085-48958086	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
12	rs552437149	chr3:48958114-48958115	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
13	rs570915677	chr3:48958191-48958192	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
14	rs111525271	chr3:48958280-48958281	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
15	rs539397458	chr3:48958319-48958320	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
16	rs528680247	chr3:48958325-48958326	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
17	rs547142003	chr3:48958334-48958335	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
18	rs147248364	chr3:48958373-48958374	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
19	rs370884522	chr3:48958420-48958421	Weak transcription Strong transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
20	rs557207829	chr3:48958480-48958481	Weak transcription Strong transcription Enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
21	rs185834393	chr3:48958486-48958487	Weak transcription Strong transcription Enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
22	rs190203125	chr3:48958492-48958493	Weak transcription Strong transcription Enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	mRNA abundance
23	rs13092715	chr3:48958706-48958707	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	8 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs13070214	chr3:48958709-48958710	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
25	rs111857993	chr3:48958720-48958721	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
26	rs9856444	chr3:48958726-48958727	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
27	rs541944946	chr3:48958772-48958773	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
28	rs56122830	chr3:48958782-48958783	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
29	rs140666757	chr3:48958801-48958802	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
30	rs572851467	chr3:48958851-48958852	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	8 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
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:287 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48954800-48957800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr3:48955200-48957800	Active TSS	Colonic Mucosa	Colon
3	chr3:48955200-48957800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr3:48955200-48957800	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr3:48955200-48958200	Active TSS	GM12878-XiMat	blood
6	chr3:48955200-48958200	Active TSS	K562	blood
7	chr3:48955400-48957800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:48955400-48957800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:48955400-48957800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:48955400-48957800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:48955400-48957800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:48955400-48957800	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr3:48955400-48957800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:48955400-48957800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:48955400-48957800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr3:48955400-48957800	Active TSS	Psoas Muscle	Psoas
17	chr3:48955400-48957800	Active TSS	Right Atrium	heart
18	chr3:48955400-48957800	Active TSS	Right Ventricle	heart
19	chr3:48955400-48957800	Active TSS	NHDF-Ad	bronchial
20	chr3:48955400-48957800	Active TSS	NHLF	lung
21	chr3:48955400-48958000	Active TSS	A549	lung
22	chr3:48955600-48957800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:48955600-48957800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:48955600-48957800	Active TSS	Aorta	Aorta
25	chr3:48955600-48957800	Bivalent/Poised TSS	HepG2	liver
26	chr3:48955800-48957800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:48955800-48957800	Active TSS	Osteobl	bone
28	chr3:48956000-48957800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:48956000-48957800	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr3:48956600-48957800	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr3:48956600-48957800	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr3:48956600-48957800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr3:48956600-48957800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:48956600-48957800	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr3:48956800-48957800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr3:48956800-48957800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:48956800-48957800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr3:48956800-48957800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr3:48956800-48957800	Flanking Active TSS	Fetal Thymus	thymus
40	chr3:48957000-48957800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr3:48957000-48957800	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr3:48957000-48957800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr3:48957000-48957800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr3:48957000-48957800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr3:48957000-48957800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:48957000-48957800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:48957000-48957800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:48957000-48957800	Flanking Active TSS	Liver	Liver
49	chr3:48957000-48957800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr3:48957000-48957800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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