Variant report

Variant	nsv892829
Chromosome Location	chr9:25579842-25615456
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:25599854..25601775-chr9:97221816..97224638,2	MCF-7	breast:
2	chr9:25600112..25602415-chr9:25676030..25679232,3	MCF-7	breast:
3	chr9:25612676..25613650-chr9:25715920..25716890,2	MCF-7	breast:
4	chr9:25613138..25615070-chr9:25677040..25679432,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IFT74-4	chr9:25613547-25613770	XLOC_007305

Variant related genes	Relation type
ENSG00000198680	chromatin interactions

Extended variants
information (count: 1005 )
Associated
traits (count: 129 )

Variant overlapped rSNPs/rCNVs (count:1005 , 50 per page) page: 1 2 3 4 5 6 7 ... 21

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2498724	chr9:25579842-25579843	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs540921343	chr9:25579867-25579868	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs556148607	chr9:25579878-25579879	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs577923358	chr9:25579883-25579884	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs578151189	chr9:25579896-25579897	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs185754967	chr9:25579901-25579902	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs563698708	chr9:25579914-25579915	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs531007775	chr9:25579919-25579920	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs78649106	chr9:25579924-25579925	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs4977995	chr9:25579936-25579937	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs544597272	chr9:25579939-25579940	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs368931099	chr9:25579945-25579946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs72705050	chr9:25579960-25579961	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs546939179	chr9:25579961-25579962	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs571925295	chr9:25579967-25579968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs573198617	chr9:25579978-25579979	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs145313127	chr9:25580008-25580009	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs550939449	chr9:25580068-25580069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs191713891	chr9:25580069-25580070	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs536746593	chr9:25580073-25580074	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs561399593	chr9:25580074-25580075	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs540433438	chr9:25580083-25580084	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs1332167	chr9:25580084-25580085	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs567307122	chr9:25580165-25580166	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs534831382	chr9:25580220-25580221	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs552962344	chr9:25580272-25580273	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs577844776	chr9:25580298-25580299	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs201802511	chr9:25580317-25580318	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs141422266	chr9:25580329-25580330	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs183437187	chr9:25580336-25580337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs532514591	chr9:25580346-25580347	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs549878650	chr9:25580352-25580353	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs575758416	chr9:25580358-25580359	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs543098992	chr9:25580362-25580363	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs57922249	chr9:25580371-25580372	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs573323194	chr9:25580378-25580379	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs571618045	chr9:25580388-25580389	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs565367547	chr9:25580409-25580410	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs532826630	chr9:25580444-25580445	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs550908621	chr9:25580447-25580448	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs369347775	chr9:25580448-25580449	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs533036568	chr9:25580463-25580464	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs551700674	chr9:25580528-25580529	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs73480821	chr9:25580550-25580551	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs548632585	chr9:25580747-25580748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs562820613	chr9:25580761-25580762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs188887603	chr9:25580791-25580792	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs193082289	chr9:25580799-25580800	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs546754768	chr9:25580834-25580835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs183442827	chr9:25580839-25580840	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:129)

Disease	PMID	Source
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Medulloblastoma	21979893	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
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
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
Pancreatic cancer	21811587	CNVD
Bipolar disorder	19114987	CNVD
Barrett''s syndrome	19417022	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
polycythaemia	22829968	CNVD
Neuroblastoma	21899760	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:25577600-25583000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:25581800-25583000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:25583000-25584000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:25583000-25584600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:25584600-25585000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:25585000-25585800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:25585200-25585600	Active TSS	Psoas Muscle	Psoas
8	chr9:25585800-25590400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:25590400-25591000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:25599200-25599800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:25599400-25599800	Enhancers	Fetal Lung	lung
12	chr9:25601000-25602400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:25601200-25602400	Enhancers	Colon Smooth Muscle	Colon
14	chr9:25601800-25603400	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr9:25601800-25603800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr9:25601800-25604000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr9:25602000-25603400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr9:25602000-25603800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr9:25602200-25602400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:25602200-25602600	Enhancers	Fetal Intestine Small	intestine
21	chr9:25602200-25602800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr9:25602200-25603000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr9:25602200-25603400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr9:25602200-25603400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr9:25602200-25603400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:25602200-25603600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr9:25602200-25604400	Enhancers	Stomach Mucosa	stomach
28	chr9:25602400-25602600	Enhancers	Gastric	stomach
29	chr9:25602400-25603400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr9:25602400-25607800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:25602800-25603400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:25603000-25603400	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr9:25603400-25607800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:25603400-25608000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr9:25603400-25608000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr9:25603400-25608000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:25603400-25608000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr9:25603400-25608000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:25603600-25608000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:25603800-25608000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr9:25603800-25608000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr9:25604000-25607600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:25604200-25605000	Enhancers	Gastric	stomach
44	chr9:25607600-25608800	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr9:25607800-25608600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr9:25608000-25608200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr9:25608000-25608400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr9:25608000-25608400	Enhancers	H1 Cell Line	embryonic stem cell
49	chr9:25608000-25608400	Enhancers	H9 Cell Line	embryonic stem cell
50	chr9:25608000-25608400	Enhancers	HUES6 Cell Line	embryonic stem cell

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