Variant report

Variant	nsv946500
Chromosome Location	chr1:171238904-171243923
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:171239400-171239436	Kidney_OC	kidney:	n/a	n/a
2	CTCF	chr1:171239852-171239914	LNCaP	prostate:	n/a	chr1:171239905-171239914
3	CTCF	chr1:171239220-171239273	Spleen_OC	spleen:	n/a	n/a
4	CTCF	chr1:171239873-171239920	MCF-7	breast:	n/a	chr1:171239905-171239914
5	HEY1	chr1:171239035-171239284	K562	blood:	n/a	n/a
6	POLR2A	chr1:171239029-171239259	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:171238977-171239361	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:171238993-171239305	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:171239013-171239295	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:171238802-171239379	H1-hESC	embryonic stem cell:	n/a	n/a
11	SPI1	chr1:171242243-171242699	HL-60	blood:	n/a	chr1:171242506-171242519

Variant related genes	Relation type
FMO1	TF binding region
HMGB1P11	TF binding region

Extended variants
information (count: 185 )
Associated
traits (count: 92 )

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	rs541776282	chr1:171238919-171238920	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs559973150	chr1:171238973-171238974	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs12022278	chr1:171238986-171238987	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs145775430	chr1:171239036-171239037	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs563190320	chr1:171239046-171239047	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs530640605	chr1:171239111-171239112	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs551881208	chr1:171239157-171239158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs12058402	chr1:171239170-171239171	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs534596509	chr1:171239225-171239226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs138513535	chr1:171239238-171239239	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs568033280	chr1:171239274-171239275	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs535223998	chr1:171239311-171239312	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs556743814	chr1:171239319-171239320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs565155423	chr1:171239326-171239327	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs183707473	chr1:171239375-171239376	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs537601860	chr1:171239397-171239398	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs530773450	chr1:171239400-171239401	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs373780431	chr1:171239490-171239491	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs186678358	chr1:171239543-171239544	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs541455050	chr1:171239586-171239587	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs553676469	chr1:171239645-171239646	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs373287189	chr1:171239667-171239668	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs542401528	chr1:171239699-171239700	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs544412617	chr1:171239709-171239710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs563949103	chr1:171239714-171239715	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs372290909	chr1:171239735-171239736	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs192742136	chr1:171239773-171239774	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs184729114	chr1:171239780-171239781	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs190007504	chr1:171239789-171239790	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs181875653	chr1:171239792-171239793	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs144121267	chr1:171239823-171239824	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs116247537	chr1:171239866-171239867	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs529187705	chr1:171239885-171239886	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs370824161	chr1:171239890-171239891	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs550356067	chr1:171239936-171239937	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs569064412	chr1:171239937-171239938	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs537135554	chr1:171239941-171239942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs558976929	chr1:171239970-171239971	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs2421804	chr1:171239982-171239983	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs184815680	chr1:171239985-171239986	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs553412141	chr1:171240026-171240027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs575200691	chr1:171240043-171240044	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs542566714	chr1:171240045-171240046	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs557257525	chr1:171240076-171240077	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs147290491	chr1:171240078-171240079	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs138910595	chr1:171240082-171240083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs564158961	chr1:171240092-171240093	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs575630267	chr1:171240096-171240097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs9660083	chr1:171240105-171240106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs528179743	chr1:171240131-171240132	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	16750200	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Rett syndrome	21593744	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21829676	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Retinoblastoma	19183342	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chordoma	18071362	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	CNVD
Burkitt''s lymphoma	19759907	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Trisomy 5 syndrome	21098271	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Breast cancer	21611746	CNVD
Neuroblastoma	18923191	CNVD
Soft tissue tumor	16732325	CNVD
Cancer	17060936	CNVD
Lung cancer	16740712	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Williams-beuren syndrome	16971481	CNVD
Developmental delay	21147756	CNVD
Burkitt''s lymphoma	20823134	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Pancreatic cancer	17952125	CNVD
Myelofibrosis	22110671	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171228800-171244400	Weak transcription	Fetal Kidney	kidney
2	chr1:171236400-171243400	Weak transcription	Small Intestine	intestine
3	chr1:171237600-171241000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:171237600-171246800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:171237800-171255200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:171238200-171240600	Weak transcription	Fetal Intestine Large	intestine
7	chr1:171238600-171253600	Weak transcription	Ovary	ovary
8	chr1:171240600-171241400	ZNF genes & repeats	Fetal Intestine Large	intestine
9	chr1:171241000-171241600	Strong transcription	Fetal Intestine Small	intestine
10	chr1:171241400-171246600	Weak transcription	Fetal Intestine Large	intestine
11	chr1:171241600-171255200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:171243400-171243600	Active TSS	Small Intestine	intestine

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