Variant report

Variant	esv3463324
Chromosome Location	chr3:42639905-42640813
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:42640335-42640432	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr3:42640230-42640274	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:42640283-42640328	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:42640328-42640329	K562	blood:	n/a	n/a
5	TBL1XR1	chr3:42640340-42640351	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
2	chr3:42640361..42643591-chr3:42693270..42696162,5	K562	blood:
3	chr3:42622208..42623993-chr3:42640628..42642693,2	MCF-7	breast:
4	chr3:42619900..42621497-chr3:42638395..42640003,2	MCF-7	breast:
5	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:
6	chr3:42640678..42643591-chr3:42694568..42696079,2	K562	blood:
7	chr3:42621283..42625330-chr3:42639303..42643596,7	MCF-7	breast:
8	chr3:42639395..42643636-chr3:42699754..42702498,4	K562	blood:

No data

Variant related genes	Relation type
NKTR	TF binding region
ENSG00000114853	chromatin interactions
ENSG00000008324	chromatin interactions
ENSG00000093183	chromatin interactions
ENSG00000230084	chromatin interactions

Extended variants
information (count: 40 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:40 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs138480981	chr3:42639933-42639934	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs576743617	chr3:42639960-42639961	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs536036639	chr3:42639962-42639963	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs149258621	chr3:42639976-42639977	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs557580230	chr3:42639979-42639980	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs572060267	chr3:42640043-42640044	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs540681155	chr3:42640124-42640125	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs557297555	chr3:42640135-42640136	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs78167645	chr3:42640225-42640226	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs543342136	chr3:42640227-42640228	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs563229086	chr3:42640274-42640275	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs188499306	chr3:42640296-42640297	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs138246973	chr3:42640316-42640317	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs113267661	chr3:42640329-42640330	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs562047774	chr3:42640332-42640333	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs527748476	chr3:42640354-42640355	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs77291243	chr3:42640385-42640386	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs3111313	chr3:42640394-42640395	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs375252028	chr3:42640396-42640397	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
20	rs533347847	chr3:42640400-42640401	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
21	rs201375436	chr3:42640419-42640420	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
22	rs3111312	chr3:42640422-42640423	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	mRNA abundance
23	rs548206736	chr3:42640430-42640431	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
24	rs570324950	chr3:42640439-42640440	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs369545015	chr3:42640440-42640441	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs572172729	chr3:42640458-42640459	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs78478610	chr3:42640471-42640472	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs79469803	chr3:42640472-42640473	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs138069697	chr3:42640514-42640515	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs193099999	chr3:42640518-42640519	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs565654054	chr3:42640608-42640609	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
32	rs534688215	chr3:42640614-42640615	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
33	rs372301111	chr3:42640629-42640630	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
34	rs546273227	chr3:42640650-42640651	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
35	rs184784637	chr3:42640656-42640657	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
36	rs556886614	chr3:42640673-42640674	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
37	rs564461731	chr3:42640678-42640679	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
38	rs542470301	chr3:42640700-42640701	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
39	rs188339566	chr3:42640701-42640702	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
40	rs528250088	chr3:42640739-42640740	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:88)

Disease	PMID	Source
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
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
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
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
Wilms tumour	17204608	CNVD
Biliary cancer	19435499	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-small cell lung cancer	21829676	CNVD
Kartagener syndrome	16639409	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Breast cancer	21509527	CNVD
Melanoma	21693616	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21364760	CNVD
abnormal development	18461090	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:135 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42633200-42641400	Weak transcription	Aorta	Aorta
2	chr3:42633200-42641600	Weak transcription	Gastric	stomach
3	chr3:42633400-42641200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:42633400-42641200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:42633400-42641200	Weak transcription	HSMMtube	muscle
6	chr3:42633400-42641400	Weak transcription	Ovary	ovary
7	chr3:42633400-42641400	Weak transcription	Psoas Muscle	Psoas
8	chr3:42633400-42641400	Weak transcription	Right Ventricle	heart
9	chr3:42633400-42641600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:42633400-42641600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:42633400-42641600	Weak transcription	Esophagus	oesophagus
12	chr3:42633400-42641600	Weak transcription	Spleen	Spleen
13	chr3:42633600-42641200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:42633600-42641200	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:42633600-42641200	Weak transcription	Fetal Kidney	kidney
16	chr3:42633600-42641200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:42633600-42641200	Weak transcription	Right Atrium	heart
18	chr3:42633600-42641200	Weak transcription	NHEK	skin
19	chr3:42633600-42641400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:42633600-42641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:42633600-42641400	Weak transcription	Brain Anterior Caudate	brain
22	chr3:42633600-42641600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:42633600-42641600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:42633600-42641600	Weak transcription	Pancreas	Pancrea
25	chr3:42633800-42641200	Weak transcription	Brain Germinal Matrix	brain
26	chr3:42634000-42641200	Weak transcription	Fetal Intestine Small	intestine
27	chr3:42634000-42641600	Weak transcription	Lung	lung
28	chr3:42634400-42641200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:42634600-42641200	Weak transcription	Fetal Brain Male	brain
30	chr3:42635400-42641200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:42635400-42641200	Weak transcription	Brain Angular Gyrus	brain
32	chr3:42635600-42640800	Weak transcription	Hela-S3	cervix
33	chr3:42635600-42641200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:42635600-42641200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:42635600-42641200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:42635600-42641200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:42635600-42641200	Weak transcription	Fetal Stomach	stomach
38	chr3:42635600-42641200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:42635600-42641400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:42635600-42641600	Weak transcription	Small Intestine	intestine
41	chr3:42635800-42641200	Weak transcription	HepG2	liver
42	chr3:42636000-42641200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:42636000-42641200	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:42636000-42641200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:42636000-42641400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:42636200-42641200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr3:42636200-42641200	Weak transcription	A549	lung
48	chr3:42636400-42640800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:42636400-42641200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:42636400-42641200	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links