Variant report

Variant	nsv540100
Chromosome Location	chr9:25170659-25633419
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:33)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:33 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:25490280..25493000-chr9:25503726..25505680,2	MCF-7	breast:
2	chr9:25599854..25601775-chr9:97221816..97224638,2	MCF-7	breast:
3	chr9:25490280..25493000-chr9:25503726..25505680,2	MCF-7	breast:
4	chr9:25450846..25453685-chr9:25454705..25457278,2	MCF-7	breast:
5	chr9:25346387..25349185-chr9:25351167..25353046,2	MCF-7	breast:
6	chr9:25175084..25177209-chr9:25178097..25179794,2	MCF-7	breast:
7	chr9:25613138..25615070-chr9:25677040..25679432,2	MCF-7	breast:
8	chr9:25478036..25481264-chr9:25482615..25485278,3	MCF-7	breast:
9	chr9:25478036..25481264-chr9:25482615..25485278,3	MCF-7	breast:
10	chr9:25321931..25322446-chr9:25349957..25350559,2	MCF-7	breast:
11	chr9:25408828..25410955-chr9:25413147..25416054,3	MCF-7	breast:
12	chr9:25267661..25270080-chr9:25677540..25679201,2	MCF-7	breast:
13	chr9:25600112..25602415-chr9:25676030..25679232,3	MCF-7	breast:
14	chr9:25415705..25417320-chr9:25422040..25423787,2	MCF-7	breast:
15	chr9:25292451..25293431-chr9:25673511..25674229,2	MCF-7	breast:
16	chr9:25415705..25417320-chr9:25422040..25423787,2	MCF-7	breast:
17	chr9:25350133..25352434-chr9:25677647..25679713,3	MCF-7	breast:
18	chr9:25450846..25453685-chr9:25454705..25457278,2	MCF-7	breast:
19	chr9:25175084..25177209-chr9:25178097..25179794,2	MCF-7	breast:
20	chr9:25612676..25613650-chr9:25715920..25716890,2	MCF-7	breast:
21	chr9:25352690..25354379-chr9:25676635..25678931,2	MCF-7	breast:
22	chr9:25408828..25410955-chr9:25413147..25416054,3	MCF-7	breast:
23	chr9:25518647..25520597-chr9:25677256..25680213,2	MCF-7	breast:
24	chr9:25448185..25450163-chr9:25451079..25453175,2	MCF-7	breast:
25	chr9:25349920..25350511-chr9:25716130..25716944,2	MCF-7	breast:
26	chr9:25321931..25322446-chr9:25349957..25350559,2	MCF-7	breast:
27	chr9:24613953..24614528-chr9:25350122..25350850,2	MCF-7	breast:
28	chr9:25448185..25450163-chr9:25451079..25453175,2	MCF-7	breast:
29	chr9:25517372..25520682-chr9:25675267..25678566,4	MCF-7	breast:
30	chr9:25261310..25262090-chr9:25716255..25716920,2	MCF-7	breast:
31	chr9:25418497..25420216-chr9:25675741..25678077,2	MCF-7	breast:
32	chr9:25515475..25518346-chr9:25676938..25679402,2	MCF-7	breast:
33	chr9:25346387..25349185-chr9:25351167..25353046,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IFT74-4	chr9:25617639-25617675	XLOC_007305
2	lnc-IFT74-4	chr9:25613547-25613770	XLOC_007305
3	lnc-TUSC1-1	chr9:25290336-25290489	NONHSAT130499
4	lnc-TUSC1-1	chr9:25288488-25288555	NONHSAT130499

No data

Variant related genes	Relation type
ENSG00000198680	chromatin interactions

Extended variants
information (count: 6972 )
Associated
traits (count: 153 )

Variant overlapped rSNPs/rCNVs (count:6972 , 50 per page) page: 1 2 3 4 5 6 7 ... 140

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs558404840	chr9:25177873-25177874	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs571834857	chr9:25177874-25177875	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs13286731	chr9:25177882-25177883	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs3126939	chr9:25177884-25177885	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs574041413	chr9:25177889-25177890	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs78141814	chr9:25177899-25177900	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs570967706	chr9:25177908-25177909	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs556239912	chr9:25177912-25177913	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs79168858	chr9:25177950-25177951	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs12337162	chr9:25178032-25178033	ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs186361870	chr9:25178033-25178034	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs191218428	chr9:25178067-25178068	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs12337176	chr9:25178084-25178085	ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs561076599	chr9:25178085-25178086	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs529713913	chr9:25178092-25178093	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs549752784	chr9:25178097-25178098	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs1925509	chr9:25178137-25178138	ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs10966779	chr9:25178148-25178149	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs532045729	chr9:25178152-25178153	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs535902219	chr9:25178185-25178186	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs150869494	chr9:25178196-25178197	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs139678939	chr9:25178218-25178219	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs534435461	chr9:25178270-25178271	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs570410177	chr9:25178273-25178274	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs567754396	chr9:25178295-25178296	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs536323300	chr9:25178334-25178335	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs144432419	chr9:25178354-25178355	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs370575807	chr9:25178414-25178415	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs146694738	chr9:25178430-25178431	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs538624138	chr9:25178499-25178500	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs181354498	chr9:25178515-25178516	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs571996605	chr9:25178523-25178524	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs537633462	chr9:25178524-25178525	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs540834169	chr9:25178536-25178537	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs1886716	chr9:25178540-25178541	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs574497688	chr9:25178542-25178543	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs185836962	chr9:25178548-25178549	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs563380074	chr9:25178556-25178557	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs190638448	chr9:25178644-25178645	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs552195040	chr9:25178712-25178713	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs72702078	chr9:25178770-25178771	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs527943988	chr9:25178777-25178778	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs139244967	chr9:25178780-25178781	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs541537471	chr9:25178807-25178808	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs567726783	chr9:25178861-25178862	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs73469976	chr9:25178863-25178864	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs550036494	chr9:25178917-25178918	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs570130164	chr9:25178935-25178936	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs538686369	chr9:25178976-25178977	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs9408057	chr9:25201666-25201667	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:153)

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
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
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	21858162	CNVD
Breast cancer	21364760	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Lung cancer	21569311	CNVD
Pancreatic cancer	21811587	CNVD
Renal cell carcinoma	21215367	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
early-passage human iPS cells	21368824	CNVD
Cancer	21215367	CNVD
Chordoma	21215367	CNVD
Bipolar disorder	19114987	CNVD
Non-small cell lung cancer	16651412	CNVD
Barrett''s syndrome	19417022	CNVD
polycythaemia	22829968	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:361 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:25177800-25178200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:25178000-25179000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr9:25201600-25204600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:25204400-25205000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:25204400-25205200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:25204600-25205200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr9:25204600-25205600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr9:25204600-25205800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr9:25204800-25206400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr9:25205000-25205600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:25205000-25206000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr9:25205000-25206200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:25205000-25206400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:25205200-25205400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr9:25205200-25205600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr9:25205400-25205600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr9:25205600-25205800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr9:25205600-25206000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr9:25205600-25206000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr9:25205600-25206000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr9:25205600-25206000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr9:25205800-25206400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr9:25206000-25206400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr9:25206000-25206400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr9:25206000-25206400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr9:25206200-25206800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:25206400-25207400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr9:25206400-25207400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:25206800-25208200	Enhancers	Liver	Liver
30	chr9:25207400-25207600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr9:25207400-25208400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr9:25208200-25209200	Weak transcription	Liver	Liver
33	chr9:25209200-25209800	Enhancers	Liver	Liver
34	chr9:25210600-25210800	Enhancers	Brain Germinal Matrix	brain
35	chr9:25210800-25212400	Weak transcription	Brain Germinal Matrix	brain
36	chr9:25212200-25212600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr9:25212400-25212800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:25212400-25212800	Enhancers	Brain Germinal Matrix	brain
39	chr9:25226000-25226600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
40	chr9:25226200-25226800	ZNF genes & repeats	Pancreas	Pancrea
41	chr9:25226600-25227000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
42	chr9:25226600-25227000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
43	chr9:25226600-25227600	Enhancers	H1 Cell Line	embryonic stem cell
44	chr9:25226800-25227200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
45	chr9:25227000-25227200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr9:25227000-25227200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr9:25227200-25227400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr9:25227200-25227400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr9:25227200-25227400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr9:25227400-25227600	Enhancers	H9 Cell Line	embryonic stem cell

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