Variant report

Variant	esv3375331
Chromosome Location	chr9:3502977-3505825
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:3500140..3503117-chr9:3505256..3509401,4	K562	blood:
2	chr9:3501077..3503324-chr9:3523015..3525744,2	MCF-7	breast:
3	chr9:3505495..3510523-chr9:3529335..3535947,8	K562	blood:
4	chr9:3500140..3503117-chr9:3505256..3509401,4	K562	blood:

Extended variants
information (count: 185 )
Associated
traits (count: 105 )

Variant overlapped rSNPs/rCNVs (count:185 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs576661778	chr9:3502996-3502997	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs545132464	chr9:3503036-3503037	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs71508567	chr9:3503041-3503042	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs527302974	chr9:3503050-3503051	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs139228983	chr9:3503161-3503162	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs560922546	chr9:3503177-3503178	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs529983250	chr9:3503186-3503187	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs192475879	chr9:3503192-3503193	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs569525035	chr9:3503206-3503207	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs543146836	chr9:3503219-3503220	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs561727994	chr9:3503220-3503221	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs149565547	chr9:3503242-3503243	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs115383683	chr9:3503295-3503296	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs77378171	chr9:3503301-3503302	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs7857554	chr9:3503324-3503325	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs144583855	chr9:3503370-3503371	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs144535388	chr9:3503392-3503393	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs4008807	chr9:3503396-3503397	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs573972230	chr9:3503443-3503444	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs111787047	chr9:3503453-3503454	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs188645782	chr9:3503456-3503457	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs576723378	chr9:3503459-3503460	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs181128434	chr9:3503469-3503470	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs565454028	chr9:3503516-3503517	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs572080672	chr9:3503609-3503610	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs541111096	chr9:3503628-3503629	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs148488278	chr9:3503632-3503633	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs529651532	chr9:3503655-3503656	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs139950041	chr9:3503666-3503667	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs549681561	chr9:3503713-3503714	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs533295629	chr9:3503738-3503739	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs184420840	chr9:3503744-3503745	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs532255290	chr9:3503759-3503760	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs551990097	chr9:3503764-3503765	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs10123592	chr9:3503793-3503794	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs534082353	chr9:3503803-3503804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs57597149	chr9:3503831-3503832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs201173268	chr9:3503835-3503836	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs35115041	chr9:3503863-3503864	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs536613638	chr9:3503870-3503871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs182434520	chr9:3503882-3503883	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs79773676	chr9:3503888-3503889	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs376390840	chr9:3503910-3503911	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs145216990	chr9:3503915-3503916	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs540778644	chr9:3503944-3503945	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs554615724	chr9:3503947-3503948	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs574118584	chr9:3503976-3503977	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs543044023	chr9:3503995-3503996	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs116570031	chr9:3504008-3504009	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs532315646	chr9:3504022-3504023	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:105)

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
Autism	20808228	CNVD
Pancreatic cancer	17952125	CNVD
T-cell lymphomas	22341440	CNVD
Breast cancer	22522925	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3474400-3524400	Weak transcription	Thymus	Thymus
2	chr9:3479200-3507200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:3479400-3508000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:3479800-3508800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:3479800-3511600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:3480000-3506400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:3480400-3508000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr9:3480600-3508800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:3480600-3510000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:3480600-3524600	Weak transcription	Left Ventricle	heart
11	chr9:3480800-3507400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:3483200-3508400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:3484800-3504200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:3484800-3507200	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:3485000-3507400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr9:3485200-3507800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:3490000-3508000	Weak transcription	Primary B cells from cord blood	blood
18	chr9:3498600-3503000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:3498800-3508600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:3499000-3508600	Weak transcription	HSMM	muscle
21	chr9:3499200-3508800	Weak transcription	HSMMtube	muscle
22	chr9:3500000-3508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr9:3500200-3505800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:3500200-3508800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:3500400-3505600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:3500400-3505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:3500400-3505800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:3500400-3507200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:3500400-3507400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:3500400-3507800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:3500400-3507800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:3500400-3507800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr9:3500400-3508400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:3500400-3508600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr9:3500400-3516800	Weak transcription	Psoas Muscle	Psoas
36	chr9:3500800-3505600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:3500800-3505600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr9:3500800-3507800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:3501000-3506800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:3501000-3508800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:3501000-3508800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:3501200-3507400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr9:3501800-3503000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:3502600-3503200	Flanking Active TSS	A549	lung
45	chr9:3502600-3503200	ZNF genes & repeats	GM12878-XiMat	blood
46	chr9:3502600-3503600	Enhancers	NH-A	brain
47	chr9:3502800-3503200	Enhancers	Osteobl	bone
48	chr9:3503000-3503600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:3503000-3505800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:3503000-3524400	Weak transcription	Fetal Thymus	thymus

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