Variant report

Variant	nsv892076
Chromosome Location	chr9:2645651-2653719
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	chr9:2645487-2645953	GM12878	blood:	n/a	n/a
2	ATF2	chr9:2645589-2645993	GM12878	blood:	n/a	n/a
3	BATF	chr9:2645607-2645877	GM12878	blood:	n/a	n/a
4	BCLAF1	chr9:2645521-2645909	GM12878	blood:	n/a	chr9:2645751-2645760
5	BHLHE40	chr9:2645681-2645899	GM12878	blood:	n/a	n/a
6	CHD2	chr9:2645560-2645796	GM12878	blood:	n/a	n/a
7	CTCF	chr9:2645822-2645871	GM13976	blood:	n/a	n/a
8	CTCF	chr9:2645792-2645892	GM12878	blood:	n/a	n/a
9	CTCF	chr9:2645800-2645912	GM13977	blood:	n/a	n/a
10	CTCF	chr9:2645632-2646055	GM12878	blood:	n/a	n/a
11	CUX1	chr9:2645679-2645907	GM12878	blood:	n/a	n/a
12	EBF1	chr9:2645644-2645898	GM12878	blood:	n/a	n/a
13	EP300	chr9:2645575-2645932	GM12878	blood:	n/a	chr9:2645751-2645765
14	EP300	chr9:2645747-2645896	GM12878	blood:	n/a	chr9:2645751-2645765
15	FOXM1	chr9:2645482-2645889	GM12878	blood:	n/a	n/a
16	IKZF1	chr9:2645635-2646006	GM12878	blood:	n/a	n/a
17	IRF4	chr9:2645581-2645887	GM12878	blood:	n/a	n/a
18	IRF4	chr9:2645523-2645941	GM12878	blood:	n/a	n/a
19	JUND	chr9:2649670-2649726	HepG2	liver:	n/a	n/a
20	MEF2A	chr9:2645582-2646046	GM12878	blood:	n/a	chr9:2646011-2646032 chr9:2646016-2646030 chr9:2645753-2645761
21	MEF2C	chr9:2645495-2645933	GM12878	blood:	n/a	chr9:2645753-2645761 chr9:2645705-2645720
22	MTA3	chr9:2645469-2645932	GM12878	blood:	n/a	n/a
23	NFATC1	chr9:2645489-2645898	GM12878	blood:	n/a	n/a
24	NFIC	chr9:2645497-2645980	GM12878	blood:	n/a	n/a
25	PBX3	chr9:2645650-2645854	GM12878	blood:	n/a	n/a
26	POLR2A	chr9:2649600-2649674	MCF10A-Er-Src	breast:	n/a	n/a
27	RAD21	chr9:2645612-2646004	GM12878	blood:	n/a	n/a
28	RAD21	chr9:2645638-2645936	GM12878	blood:	n/a	n/a
29	RAD21	chr9:2645621-2645895	GM12878	blood:	n/a	n/a
30	REST	chr9:2645617-2645825	Hela-S3	cervix:	n/a	n/a
31	RUNX3	chr9:2645486-2645918	GM12878	blood:	n/a	n/a
32	RUNX3	chr9:2645427-2645992	GM12878	blood:	n/a	n/a
33	SMC3	chr9:2645587-2646016	GM12878	blood:	n/a	n/a
34	SP1	chr9:2645588-2645868	GM12878	blood:	n/a	n/a
35	SPI1	chr9:2645644-2645855	GM12878	blood:	n/a	chr9:2645751-2645760
36	SPI1	chr9:2645530-2645909	GM12891	blood:	n/a	chr9:2645751-2645760
37	SPI1	chr9:2645524-2645933	GM12878	blood:	n/a	chr9:2645904-2645913 chr9:2645751-2645760
38	SPI1	chr9:2645521-2645948	GM12891	blood:	n/a	chr9:2645904-2645913 chr9:2645751-2645760
39	SPI1	chr9:2645320-2645872	GM12878	blood:	n/a	chr9:2645751-2645760
40	STAT3	chr9:2653297-2653395	MCF10A-Er-Src	breast:	n/a	n/a
41	TBL1XR1	chr9:2645640-2645936	GM12878	blood:	n/a	n/a
42	WRNIP1	chr9:2645367-2645653	GM12878	blood:	n/a	n/a
43	WRNIP1	chr9:2652832-2652865	GM12878	blood:	n/a	n/a
44	ZNF143	chr9:2645667-2645867	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2642588..2644661-chr9:2646900..2649864,2	K562	blood:

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	VLDLR	hsa-miR-130b-3p	chr9:2648316-2648335

Variant related genes	Relation type
ENSG00000236404	TF binding region
VLDLR	TF binding region

Extended variants
information (count: 467 )
Associated
traits (count: 104 )

Variant overlapped rSNPs/rCNVs (count:467 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs34753566	chr9:2645651-2645652	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
2	rs78342396	chr9:2645655-2645656	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
3	rs554072220	chr9:2645673-2645674	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
4	rs573868499	chr9:2645692-2645693	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
5	rs144724569	chr9:2645713-2645714	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
6	rs6143	chr9:2645719-2645720	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs200483246	chr9:2645734-2645735	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
8	rs141757226	chr9:2645735-2645736	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
9	rs372491770	chr9:2645740-2645741	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
10	rs568955387	chr9:2645767-2645768	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
11	rs35847091	chr9:2645773-2645774	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs369458672	chr9:2645778-2645779	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
13	rs34622158	chr9:2645795-2645796	Strong transcription Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs533601459	chr9:2645856-2645857	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
15	rs34961825	chr9:2645870-2645871	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs563770253	chr9:2645882-2645883	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
17	rs34534826	chr9:2645890-2645891	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
18	rs150716556	chr9:2645895-2645896	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
19	rs530981036	chr9:2645907-2645908	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
20	rs548522211	chr9:2645981-2645982	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
21	rs568555343	chr9:2645983-2645984	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
22	rs537546636	chr9:2645994-2645995	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
23	rs374327920	chr9:2645997-2645998	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
24	rs139145148	chr9:2646021-2646022	Strong transcription Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
25	rs571342210	chr9:2646059-2646060	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs187135086	chr9:2646088-2646089	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs35452784	chr9:2646107-2646108	Strong transcription Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs117120017	chr9:2646144-2646145	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs538130024	chr9:2646180-2646181	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs557729167	chr9:2646184-2646185	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs143015647	chr9:2646185-2646186	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs528705611	chr9:2646186-2646187	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs192158490	chr9:2646193-2646194	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs111451365	chr9:2646200-2646201	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs571204796	chr9:2646220-2646221	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs35037163	chr9:2646269-2646270	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs41271163	chr9:2646293-2646294	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs146156696	chr9:2646322-2646323	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs372468631	chr9:2646342-2646343	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs116467449	chr9:2646376-2646377	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs182216426	chr9:2646381-2646382	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs184905581	chr9:2646390-2646391	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs369197633	chr9:2646395-2646396	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs556814765	chr9:2646401-2646402	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs373695454	chr9:2646416-2646417	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs377669923	chr9:2646444-2646445	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs146258996	chr9:2646445-2646446	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs148487944	chr9:2646492-2646493	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs370936675	chr9:2646495-2646496	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs200479365	chr9:2646500-2646501	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:104)

Disease	PMID	Source
Gastric cancer	16715143	CNVD
Glioblastoma multiforme	22286061	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Disorders of sex development	21048976	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Autism	20531469	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21373258	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Schizophrenia	23813976	CNVD
Ovarian cancer	22355333	CNVD
Schizophrenia	20967226	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Renal cell carcinoma	21215367	CNVD

Chromatin state (count:175 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2627200-2648400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:2633200-2646000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:2633600-2656600	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:2634400-2648200	Weak transcription	Placenta	Placenta
5	chr9:2635000-2652600	Strong transcription	Dnd41	blood
6	chr9:2635200-2655000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:2635200-2656200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:2635400-2656000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:2635400-2656800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:2635400-2656800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:2635600-2647600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:2635600-2655000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:2635800-2656000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:2635800-2657800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:2637400-2654400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:2638000-2654400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:2638000-2656400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr9:2638400-2655800	Strong transcription	Fetal Lung	lung
19	chr9:2638400-2656400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:2638600-2653600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:2638600-2655400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:2638600-2655800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr9:2638800-2656000	Strong transcription	Fetal Muscle Leg	muscle
24	chr9:2639000-2650800	Weak transcription	HSMM	muscle
25	chr9:2639000-2655800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr9:2639200-2655200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:2639400-2646600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:2639600-2654800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:2639800-2654200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:2639800-2655200	Strong transcription	Brain Cingulate Gyrus	brain
31	chr9:2639800-2656000	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr9:2639800-2656000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:2640000-2650800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:2640000-2655000	Strong transcription	Left Ventricle	heart
35	chr9:2640000-2655600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:2640000-2655600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr9:2640000-2662200	Weak transcription	Right Atrium	heart
38	chr9:2640200-2653800	Strong transcription	Brain Anterior Caudate	brain
39	chr9:2640200-2654200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr9:2640200-2655400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:2640200-2656200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:2640800-2655800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:2640800-2655800	Strong transcription	Adipose Nuclei	Adipose
44	chr9:2641000-2653800	Weak transcription	HepG2	liver
45	chr9:2641000-2655600	Strong transcription	Brain Hippocampus Middle	brain
46	chr9:2641200-2654000	Strong transcription	Fetal Kidney	kidney
47	chr9:2641400-2655600	Strong transcription	Fetal Brain Female	brain
48	chr9:2641400-2668400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:2641600-2654800	Weak transcription	NHDF-Ad	bronchial
50	chr9:2642000-2654800	Weak transcription	Muscle Satellite Cultured Cells	--

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