Variant report

Variant	nsv972424
Chromosome Location	chr9:97884806-97886925
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	CEBPB	chr9:97885996-97886090	IMR90	lung:	n/a	n/a
2	CEBPB	chr9:97886020-97886169	K562	blood:	n/a	n/a
3	CTCF	chr9:97886873-97887288	MCF-7	breast:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
4	CTCF	chr9:97886920-97887070	AG10803	skin:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
5	CTCF	chr9:97886702-97887293	SK-N-SH	brain:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
6	CTCF	chr9:97886824-97887188	H1-hESC	embryonic stem cell:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
7	CTCF	chr9:97886920-97887070	BE2_C	brain:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
8	CTCF	chr9:97886872-97887177	K562	blood:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
9	CTCF	chr9:97886840-97886990	NHDF-neo	bronchial:	n/a	n/a
10	CTCF	chr9:97886920-97887070	GM12873	blood:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
11	CTCF	chr9:97886820-97886970	GM12864	blood:	n/a	n/a
12	CTCF	chr9:97886915-97887150	K562	blood:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
13	CTCF	chr9:97886855-97887127	H1-hESC	embryonic stem cell:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
14	CTCF	chr9:97886870-97887147	SK-N-SH_RA	brain:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
15	CTCF	chr9:97886900-97887050	HRE	kidney:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
16	CTCF	chr9:97886700-97886850	GM12872	blood:	n/a	n/a
17	CTCF	chr9:97886838-97887212	A549	lung:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
18	CTCF	chr9:97886920-97887070	HCM	heart:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
19	CTCF	chr9:97886920-97887070	AG04450	lung:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
20	CTCF	chr9:97886840-97886990	GM06990	blood:	n/a	n/a
21	CTCF	chr9:97886640-97886790	AG04449	skin:	n/a	n/a
22	CTCF	chr9:97886900-97887050	MCF-7	breast:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
23	CTCF	chr9:97886859-97887152	HepG2	liver:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
24	CTCF	chr9:97886900-97887050	GM12865	blood:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
25	CTCF	chr9:97886920-97887070	BJ	skin:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
26	CTCF	chr9:97886920-97887070	GM12868	blood:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
27	CTCF	chr9:97886814-97887301	MCF-7	breast:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
28	CTCF	chr9:97886880-97887030	WI-38	lung:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
29	CTCF	chr9:97886620-97886770	WERI-Rb-1	eye:	n/a	n/a
30	CTCF	chr9:97886860-97887010	HAc	cerebellar:	n/a	n/a
31	CTCF	chr9:97886900-97887050	GM12864	blood:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
32	CTCF	chr9:97886920-97887070	HEK293	kidney:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
33	CTCF	chr9:97886840-97886990	HFF	foreskin:	n/a	n/a
34	CTCF	chr9:97886914-97887185	K562	blood:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
35	CTCF	chr9:97886900-97887050	HMF	breast:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
36	CTCF	chr9:97886865-97887174	A549	lung:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
37	CTCF	chr9:97886880-97887213	GM12878	blood:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
38	CTCF	chr9:97886900-97887050	GM12866	blood:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
39	CTCF	chr9:97886920-97887070	NHLF	lung:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
40	CTCF	chr9:97886780-97886930	K562	blood:	n/a	n/a
41	CTCF	chr9:97886920-97887070	HPAF	blood vessel:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
42	CTCF	chr9:97886770-97887265	HCT-116	colon:	n/a	chr9:97887008-97887026 chr9:97887010-97887023
43	GATA2	chr9:97886733-97887233	SH-SY5Y	brain:	n/a	n/a
44	MAX	chr9:97886877-97887276	MCF-7	breast:	n/a	n/a
45	MXI1	chr9:97886420-97888329	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr9:97886872-97887152	HepG2	liver:	n/a	n/a
47	POLR2A	chr9:97886417-97887393	A549	lung:	n/a	n/a
48	POLR2A	chr9:97885168-97885247	K562	blood:	n/a	n/a
49	POLR2A	chr9:97884634-97885448	A549	lung:	n/a	n/a
50	POLR2A	chr9:97885301-97885365	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97872344..97876290-chr9:97882000..97885153,3	MCF-7	breast:
2	chr9:97883295..97885445-chr9:97887654..97889773,2	MCF-7	breast:
3	chr9:97854598..97856829-chr9:97883315..97884818,2	MCF-7	breast:
4	chr9:97883098..97885141-chr9:97887172..97889883,3	K562	blood:
5	chr9:97443387..97444120-chr9:97886736..97887568,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf3-2	chr9:97885803-97886150	NONHSAT133357

Variant related genes	Relation type
ENSG00000223849	TF binding region
ENSG00000229065	chromatin interactions
ENSG00000158169	chromatin interactions

Extended variants
information (count: 84 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:84 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs570714720	chr9:97884846-97884847	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs535119212	chr9:97884865-97884866	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs553185247	chr9:97884866-97884867	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs185822123	chr9:97884879-97884880	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs73528483	chr9:97884948-97884949	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs142374839	chr9:97884992-97884993	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs151274551	chr9:97884993-97884994	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs546142264	chr9:97884995-97884996	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs557739378	chr9:97884996-97884997	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs73528484	chr9:97885073-97885074	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs16911980	chr9:97885119-97885120	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs139289637	chr9:97885162-97885163	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs550633370	chr9:97885163-97885164	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs73528487	chr9:97885166-97885167	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs377715756	chr9:97885373-97885374	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs189558814	chr9:97885406-97885407	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs371361958	chr9:97885411-97885412	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs181055320	chr9:97885440-97885441	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs533273167	chr9:97885573-97885574	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs185996262	chr9:97885602-97885603	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs881791	chr9:97885616-97885617	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs528463482	chr9:97885629-97885630	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs190852995	chr9:97885643-97885644	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs568239745	chr9:97885730-97885731	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs555066867	chr9:97885774-97885775	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs535524203	chr9:97885788-97885789	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs149725444	chr9:97885831-97885832	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs569063409	chr9:97885846-97885847	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs146720279	chr9:97885868-97885869	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs566974788	chr9:97885873-97885874	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs183354123	chr9:97885897-97885898	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs368201235	chr9:97885983-97885984	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs146108049	chr9:97886025-97886026	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs572830976	chr9:97886057-97886058	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs28565379	chr9:97886061-97886062	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs186119389	chr9:97886062-97886063	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs190632122	chr9:97886110-97886111	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs372471372	chr9:97886113-97886114	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs370994431	chr9:97886129-97886130	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs374630094	chr9:97886147-97886148	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs182810178	chr9:97886159-97886160	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs139786405	chr9:97886186-97886187	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs562673362	chr9:97886209-97886210	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs577756669	chr9:97886212-97886213	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs545324255	chr9:97886230-97886231	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs373839399	chr9:97886235-97886236	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs4647520	chr9:97886259-97886260	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs879559	chr9:97886312-97886313	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs561708485	chr9:97886348-97886349	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs77734513	chr9:97886352-97886353	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Bipolar disorder	18458673	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Wilms tumour	21544195	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Biliary cancer	19435499	CNVD
small cell lung cancer	20016488	CNVD
Intracranial aneurysm	16715129	CNVD
Cardiac fibroma	18329553	CNVD
Breast cancer	17133270	CNVD
Basal cell nevus syndrome	21572526	CNVD
Mental retardation	19951919	CNVD
Retinoblastoma	22278416	CNVD
9q22.3 microdeletion syndrome	22283845	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Microcephaly	18830227	CNVD
overgrowth syndrome	16570072	CNVD
Effusion lymphoma	18079361	CNVD

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr9:97861200-97889800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:97866000-97889600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:97866200-97889600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:97866400-97886600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:97868600-97889400	Weak transcription	Fetal Heart	heart
7	chr9:97869800-97886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:97869800-97889800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr9:97870400-97889600	Weak transcription	Fetal Thymus	thymus
10	chr9:97870600-97889800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:97874600-97889400	Weak transcription	Colonic Mucosa	Colon
12	chr9:97875000-97889800	Weak transcription	Hela-S3	cervix
13	chr9:97875200-97889600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:97875200-97889600	Weak transcription	HSMMtube	muscle
15	chr9:97875400-97889400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:97875400-97889400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:97875400-97895400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:97875400-97900400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:97875600-97887800	Weak transcription	Placenta	Placenta
20	chr9:97875600-97889400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:97875600-97889600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:97875600-97889600	Weak transcription	Adipose Nuclei	Adipose
23	chr9:97875600-97900000	Weak transcription	Spleen	Spleen
24	chr9:97875600-97906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:97875800-97888800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:97875800-97892200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr9:97876800-97889600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:97877000-97886400	Weak transcription	Primary T cells from cord blood	blood
29	chr9:97877000-97886600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr9:97877000-97889600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:97877000-97889600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:97877000-97892000	Weak transcription	Gastric	stomach
33	chr9:97877000-97896400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:97877200-97885800	Weak transcription	Fetal Intestine Large	intestine
35	chr9:97879000-97889200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:97879200-97886400	Weak transcription	Lung	lung
37	chr9:97879200-97888800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:97879200-97889400	Weak transcription	HSMM	muscle
39	chr9:97879200-97889600	Weak transcription	Right Atrium	heart
40	chr9:97879400-97887000	Weak transcription	A549	lung
41	chr9:97879400-97889400	Weak transcription	Left Ventricle	heart
42	chr9:97879400-97889400	Weak transcription	Pancreas	Pancrea
43	chr9:97879600-97886800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:97879600-97887000	Weak transcription	NHEK	skin
45	chr9:97879600-97887400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:97879600-97889200	Weak transcription	Brain Substantia Nigra	brain
47	chr9:97879600-97889400	Weak transcription	Brain Angular Gyrus	brain
48	chr9:97879600-97889600	Weak transcription	Ovary	ovary
49	chr9:97879600-97890600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:97879800-97885000	Weak transcription	Esophagus	oesophagus

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