Variant report

Variant	esv3378420
Chromosome Location	chr9:24010617-24371943
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:24090178..24090821-chr9:24832388..24833273,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DMRTA1-6	chr9:24046212-24046307	XLOC_007303
2	lnc-DMRTA1-6	chr9:24146433-24146893	NONHSAT130486
3	lnc-DMRTA1-6	chr9:24046211-24046307	NONHSAT130486
4	lnc-DMRTA1-6	chr9:24146434-24146893	XLOC_007303

Extended variants
information (count: 3084 )
Associated
traits (count: 146 )

Variant overlapped rSNPs/rCNVs (count:3084 , 50 per page) page: 1 2 3 4 5 6 7 ... 62

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs73652011	chr9:24010697-24010698	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs573069602	chr9:24010715-24010716	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs535731321	chr9:24010725-24010726	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs376869936	chr9:24010729-24010730	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs538130749	chr9:24010780-24010781	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs533056893	chr9:24010855-24010856	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs555626394	chr9:24010915-24010916	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs575504054	chr9:24010941-24010942	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs138430641	chr9:24010955-24010956	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs563780940	chr9:24010964-24010965	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs111278640	chr9:24011000-24011001	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs552855007	chr9:24011028-24011029	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs577242368	chr9:24011037-24011038	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs192481198	chr9:24011253-24011254	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs551957132	chr9:24011261-24011262	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs375280734	chr9:24011291-24011292	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs1349355	chr9:24011299-24011300	Enhancers Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs184720382	chr9:24011339-24011340	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs548470097	chr9:24011361-24011362	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs528006482	chr9:24011378-24011379	Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs111775522	chr9:24011437-24011438	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs561986100	chr9:24011441-24011442	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs141368152	chr9:24011466-24011467	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs188895147	chr9:24011478-24011479	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs116516452	chr9:24011494-24011495	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs539484294	chr9:24011496-24011497	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs74333713	chr9:24011507-24011508	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs181312034	chr9:24011509-24011510	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs567602727	chr9:24011551-24011552	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs535792723	chr9:24011624-24011625	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs537887325	chr9:24011634-24011635	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs555689222	chr9:24011640-24011641	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs185574773	chr9:24011660-24011661	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs538061659	chr9:24011699-24011700	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs146987657	chr9:24011739-24011740	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs556133841	chr9:24011740-24011741	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs577302948	chr9:24011744-24011745	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs546259189	chr9:24011811-24011812	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs1450588	chr9:24011860-24011861	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs201019459	chr9:24011886-24011887	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs76785258	chr9:24011888-24011889	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs541781667	chr9:24011909-24011910	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs557948375	chr9:24011929-24011930	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs562049233	chr9:24011935-24011936	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs143733598	chr9:24011955-24011956	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs544417213	chr9:24012029-24012030	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs564686265	chr9:24012033-24012034	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs147208265	chr9:24012062-24012063	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs546671765	chr9:24012093-24012094	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs61355972	chr9:24012096-24012097	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:146)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	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
Oral squamous cell carcinoma	17134496	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
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic myeloid leukemia	21384125	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Metanephric adenoma	20802469	CNVD
Developmental delay	21147756	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	22183965	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Non-small cell lung cancer	19010865	CNVD
Myoepithelioma	18604193	CNVD
Cancer	22183965	CNVD
Glioblastoma multiforme	21569311	CNVD
Myelofibrosis	22110671	CNVD
Ewing''s sarcoma	22429812	CNVD
Neuroblastoma	21899760	CNVD
Glioblastoma multiforme	19435819	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Glioblastoma multiforme	22291905	CNVD
Lung cancer	21911935	CNVD
Primary central nervous system lymphoma	21088137	CNVD
head and neck squamous cell carcinoma	21798897	CNVD
Cancer	21253487	CNVD
Glioblastoma multiforme	22286061	CNVD
Intracranial ependymoma	16609018	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Glioblastoma multiforme	21922591	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Urothelial cell carcinoma	18451213	CNVD
Glioma	17123091	CNVD
Mental retardation	17124404	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Leukemia	19602459	CNVD
Acute monocytic leukemia	16498392	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Leukemia	18688285	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Acute myeloid leukemia	19651601	CNVD
Coronary Disease	20032323	CNVD
Squamous cell cancer	20885788	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	21732550	CNVD
Gastric cancer	22539939	CNVD
Cancer	21183584	CNVD
T-cell lymphomas	19863542	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Metastatic melanoma	18483359	CNVD
Non-small cell lung cancer	20864512	CNVD
Cervical cancer	21062161	CNVD
Acute myeloid leukemia	16864856	CNVD
Glioblastoma	17090523	CNVD
Lung cancer	16773561	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Colorectal cancer	16774939	CNVD
Bladder cancer	19088036	CNVD
Colorectal cancer	16272173	CNVD
Melanoma	16977458	CNVD
Glioblastoma multiforme	17369134	CNVD
Chagasic megaesophagus	20163722	CNVD
Melanoma	19566914	CNVD
Squamous cell cancer	19047905	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung cancer	19525976	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Melanoma	17363583	CNVD
Glioblastoma multiforme	19115005	CNVD
Adenoid cystic carcinoma	18332873	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Acute myeloid leukemia	21251322	CNVD
Oral cancer	21386901	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21858162	CNVD
early-passage human iPS cells	21368824	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Renal cell carcinoma	21215367	CNVD
Esophageal adenocarcinoma	18519675	CNVD

Chromatin state (count:198 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:24007400-24010800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:24007600-24011200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr9:24007800-24010800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:24007800-24011000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:24009800-24012400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr9:24010200-24010800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:24010200-24012200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:24010400-24011200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:24010800-24011400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr9:24010800-24011400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr9:24010800-24011600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:24010800-24012400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr9:24011000-24011600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:24011000-24012200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr9:24011000-24012400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:24011200-24011600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:24011200-24011600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr9:24011200-24011600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr9:24011200-24011600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr9:24011400-24012600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:24011600-24013000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:24011600-24013000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:24012600-24012800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr9:24023600-24025000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr9:24023600-24025200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr9:24023800-24024200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr9:24023800-24025000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr9:24024000-24024600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr9:24024200-24035200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:24024400-24024600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr9:24025000-24034600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:24025200-24025400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr9:24025200-24029600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr9:24030000-24036200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:24031000-24031800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:24032200-24032800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:24032800-24035400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:24034600-24037200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr9:24034800-24036000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr9:24035200-24035800	Enhancers	H9 Cell Line	embryonic stem cell
41	chr9:24035200-24035800	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr9:24035200-24037200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr9:24035200-24038200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr9:24035400-24036600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:24035400-24036800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr9:24035400-24037200	Enhancers	Fetal Brain Female	brain
47	chr9:24035400-24037400	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr9:24035600-24036400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr9:24035600-24036600	Enhancers	Brain Germinal Matrix	brain
50	chr9:24035600-24036800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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