Variant report

Variant	nsv562640
Chromosome Location	chr13:90276827-90355675
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	chr13:90347808..90348492-chr13:90905964..90906495,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLITRK6-26	chr13:90351476-90351493	NONHSAT034635
2	lnc-SLITRK6-26	chr13:90343642-90343795	NONHSAT034635
3	lnc-SLITRK6-26	chr13:90353649-90353765	NONHSAT034635
4	lnc-SLITRK6-26	chr13:90341209-90342696	NONHSAT034635

Extended variants
information (count: 1280 )
Associated
traits (count: 86 )

Variant overlapped rSNPs/rCNVs (count:1280 , 50 per page) page: 1 2 3 4 5 6 7 ... 26

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1016797	chr13:90276827-90276828	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs540568636	chr13:90276832-90276833	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs148098045	chr13:90276869-90276870	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs141833595	chr13:90276870-90276871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs576797227	chr13:90276904-90276905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs1016798	chr13:90276945-90276946	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs541840921	chr13:90276950-90276951	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs373957904	chr13:90276979-90276980	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs188608401	chr13:90276993-90276994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs17662405	chr13:90277002-90277003	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs561184458	chr13:90277056-90277057	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs528743736	chr13:90277059-90277060	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs555421667	chr13:90277096-90277097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs193156038	chr13:90277110-90277111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs74110451	chr13:90277132-90277133	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs536589504	chr13:90277149-90277150	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs184418591	chr13:90277150-90277151	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs188729109	chr13:90277174-90277175	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs181196091	chr13:90277189-90277190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs75994580	chr13:90277208-90277209	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs115961101	chr13:90277219-90277220	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs140063321	chr13:90277271-90277272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs118121540	chr13:90277290-90277291	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs558827800	chr13:90277307-90277308	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs576720655	chr13:90277404-90277405	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs544201609	chr13:90277448-90277449	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs116338930	chr13:90277450-90277451	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs79412083	chr13:90277468-90277469	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs541560448	chr13:90277487-90277488	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs114899786	chr13:90277499-90277500	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs564573333	chr13:90277515-90277516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs183970598	chr13:90277544-90277545	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs189429368	chr13:90277557-90277558	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs565581885	chr13:90277584-90277585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs565602391	chr13:90277603-90277604	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs369722059	chr13:90277607-90277608	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs578127062	chr13:90277620-90277621	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs532739954	chr13:90277687-90277688	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs533379104	chr13:90277766-90277767	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs17729945	chr13:90277888-90277889	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs564026459	chr13:90277907-90277908	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs114582775	chr13:90277911-90277912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs35338883	chr13:90277965-90277966	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs180725466	chr13:90278005-90278006	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs76958974	chr13:90278011-90278012	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs71444044	chr13:90278039-90278040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs533983566	chr13:90278044-90278045	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs187413867	chr13:90278062-90278063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs570724252	chr13:90278116-90278117	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs537793757	chr13:90278138-90278139	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:86)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
HIV/AIDS	22032296	CNVD
Prostate cancer	16705090	CNVD
High-proliferative meningiomas	17937814	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Chordoma	21602918	CNVD
Bladder cancer	21949216	CNVD
Acute myeloid leukemia	16864856	CNVD
Burkitt''s lymphoma	18698080	CNVD
Cancer	21637783	CNVD
Medulloblastoma	21979893	CNVD
Chronic lymphocytic leukemia	21518781	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Ovarian cancer	20844748	CNVD
Colorectal cancer	19359472	CNVD
Intracranial aneurysm	19064780	CNVD
Breast cancer	19287154	CNVD
Acute myeloid leukemia	18379011	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Multiple myeloma	17077331	CNVD
Ependymoma	16718352	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Ovarian cancer	22174824	CNVD
Myoepithelioma	18604193	CNVD
Breast cancer	17133270	CNVD
Prostate cancer	18632612	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Developmental delay	21147756	CNVD
Melanoma	18172304	CNVD
Prostate cancer	16573809	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Basal cell lymphoma	17053054	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Metanephric adenoma	20802469	CNVD
Gastric cancer	17908304	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Liposarcoma	21253554	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Acute myeloid leukemia	20729466	CNVD
abnormal development	18461090	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	21965145	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Cancer	21220470	CNVD
Cancer	21183584	CNVD
Omodysplasia	19481194	CNVD
Breast cancer	22032731	CNVD
Mantle cell lymphoma	19690137	CNVD
Rhabdomyosarcoma	17210683	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Breast cancer	21364760	CNVD
Medulloblastoma	19270706	CNVD
Myelofibrosis	22110671	CNVD
coloboma	21285886	CNVD
Cancer	20164920	CNVD
Burkitt''s lymphoma	19759907	CNVD
Wilms tumour	21544195	CNVD
Acute myeloid leukemia	19651601	CNVD
Effusion lymphoma	18079361	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:90267000-90280200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:90279800-90280200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr13:90280200-90280400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:90296600-90298800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:90298800-90300000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:90300000-90301600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:90300400-90303800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:90306000-90306600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:90312000-90313400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr13:90312800-90313600	Enhancers	HMEC	breast
11	chr13:90313400-90314200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr13:90314200-90314400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr13:90316200-90316600	Enhancers	Gastric	stomach
14	chr13:90321200-90321600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:90321200-90321800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr13:90321600-90323000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr13:90322600-90323600	Enhancers	HUVEC	blood vessel
18	chr13:90323000-90323400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr13:90323000-90323400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr13:90323000-90323600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr13:90323600-90324800	Weak transcription	HUVEC	blood vessel
22	chr13:90327800-90328000	Enhancers	Gastric	stomach
23	chr13:90327800-90328000	Enhancers	Spleen	Spleen
24	chr13:90328000-90329200	Weak transcription	HUVEC	blood vessel
25	chr13:90329200-90329800	Enhancers	HUVEC	blood vessel
26	chr13:90336400-90336800	Enhancers	Fetal Heart	heart
27	chr13:90336800-90340800	Weak transcription	Fetal Heart	heart
28	chr13:90337000-90337600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:90337200-90337800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr13:90337600-90339000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr13:90339000-90339400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:90340000-90340400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr13:90340000-90341400	Enhancers	Brain Cingulate Gyrus	brain
34	chr13:90340600-90340800	Enhancers	Brain Substantia Nigra	brain
35	chr13:90340800-90341600	Active TSS	Brain Anterior Caudate	brain
36	chr13:90340800-90341600	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr13:90340800-90341600	Enhancers	Fetal Heart	heart
38	chr13:90340800-90342200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr13:90341000-90341200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr13:90341000-90341400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr13:90341000-90341600	Enhancers	Right Atrium	heart
42	chr13:90341000-90341600	Enhancers	Right Ventricle	heart
43	chr13:90341000-90341800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr13:90341000-90341800	Enhancers	Colon Smooth Muscle	Colon
45	chr13:90341000-90342400	Enhancers	Brain Angular Gyrus	brain
46	chr13:90341000-90342400	Enhancers	Brain Hippocampus Middle	brain
47	chr13:90341200-90341400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:90341200-90341600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr13:90341200-90341600	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr13:90341200-90341600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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