Variant report

Variant	nsv998382
Chromosome Location	chr1:169899427-169929582
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	CEBPB	chr1:169915309-169915804	MCF-7	breast:	n/a	chr1:169915539-169915552 chr1:169915541-169915550
2	CEBPB	chr1:169915401-169915893	MCF-7	breast:	n/a	chr1:169915539-169915552 chr1:169915541-169915550
3	CEBPB	chr1:169920135-169920408	HepG2	liver:	n/a	chr1:169920249-169920258 chr1:169920248-169920259 chr1:169920247-169920258
4	CEBPB	chr1:169915356-169915820	Hela-S3	cervix:	n/a	chr1:169915539-169915552 chr1:169915541-169915550
5	CEBPB	chr1:169920115-169920364	K562	blood:	n/a	chr1:169920249-169920258 chr1:169920248-169920259 chr1:169920247-169920258
6	CEBPB	chr1:169920089-169920421	IMR90	lung:	n/a	chr1:169920249-169920258 chr1:169920248-169920259 chr1:169920247-169920258
7	CEBPB	chr1:169920105-169920380	A549	lung:	n/a	chr1:169920249-169920258 chr1:169920248-169920259 chr1:169920247-169920258
8	CEBPB	chr1:169915475-169915783	IMR90	lung:	n/a	chr1:169915539-169915552 chr1:169915541-169915550
9	CTCF	chr1:169914555-169914672	MCF-7	breast:	n/a	n/a
10	CTCF	chr1:169914572-169914617	MCF-7	breast:	n/a	n/a
11	CTCF	chr1:169926841-169926902	Kidney_OC	kidney:	n/a	n/a
12	CTCF	chr1:169914599-169914659	Fibrobl	skin:	n/a	n/a
13	CTCF	chr1:169914627-169914631	MCF-7	breast:	n/a	n/a
14	CTCF	chr1:169914619-169914624	MCF-7	breast:	n/a	n/a
15	CUX1	chr1:169912649-169912714	GM12878	blood:	n/a	n/a
16	E2F4	chr1:169911118-169911167	MCF10A-Er-Src	breast:	n/a	n/a
17	ELF1	chr1:169903412-169903843	MCF-7	breast:	n/a	n/a
18	ELK1	chr1:169913442-169913451	Hela-S3	cervix:	n/a	n/a
19	ELK4	chr1:169911490-169911926	Hela-S3	cervix:	n/a	chr1:169911879-169911890
20	EP300	chr1:169911550-169911955	SK-N-SH_RA	brain:	n/a	chr1:169911649-169911659
21	EP300	chr1:169901090-169901427	SK-N-SH_RA	brain:	n/a	n/a
22	EP300	chr1:169903523-169903943	Hela-S3	cervix:	n/a	n/a
23	EP300	chr1:169911556-169912032	SK-N-SH_RA	brain:	n/a	chr1:169911649-169911659
24	EP300	chr1:169922354-169922368	K562	blood:	n/a	n/a
25	EP300	chr1:169900828-169901606	SK-N-SH	brain:	n/a	chr1:169901441-169901455
26	EP300	chr1:169901020-169901447	SK-N-SH_RA	brain:	n/a	n/a
27	FOS	chr1:169911133-169911507	HUVEC	blood vessel:	n/a	chr1:169911311-169911318 chr1:169911310-169911319 chr1:169911311-169911319
28	FOS	chr1:169915443-169915573	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr1:169903180-169903925	Hela-S3	cervix:	n/a	n/a
30	FOS	chr1:169911133-169911465	MCF10A-Er-Src	breast:	n/a	chr1:169911311-169911318 chr1:169911310-169911319 chr1:169911311-169911319
31	FOS	chr1:169911131-169911433	MCF10A-Er-Src	breast:	n/a	chr1:169911311-169911318 chr1:169911310-169911319 chr1:169911311-169911319
32	FOS	chr1:169903549-169903847	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr1:169911088-169911415	MCF10A-Er-Src	breast:	n/a	chr1:169911311-169911318 chr1:169911310-169911319 chr1:169911311-169911319
34	FOS	chr1:169911148-169911489	MCF10A-Er-Src	breast:	n/a	chr1:169911311-169911318 chr1:169911310-169911319 chr1:169911311-169911319
35	FOXA1	chr1:169911491-169911950	T-47D	breast:	n/a	n/a
36	FOXA1	chr1:169911448-169911953	T-47D	breast:	n/a	n/a
37	FOXA2	chr1:169911102-169911547	A549	lung:	n/a	chr1:169911356-169911368
38	FOXM1	chr1:169903272-169904167	MCF-7	breast:	n/a	n/a
39	FOXM1	chr1:169911508-169912049	MCF-7	breast:	n/a	n/a
40	FOXP2	chr1:169903633-169903787	PFSK-1	brain:	n/a	n/a
41	GATA2	chr1:169911407-169911814	HUVEC	blood vessel:	n/a	n/a
42	GATA2	chr1:169928101-169928458	SH-SY5Y	brain:	n/a	chr1:169928371-169928381 chr1:169928243-169928255
43	GATA3	chr1:169903155-169904372	MCF-7	breast:	n/a	n/a
44	GATA3	chr1:169911410-169912015	MCF-7	breast:	n/a	n/a
45	GATA3	chr1:169918241-169918770	SK-N-SH	brain:	n/a	n/a
46	GATA3	chr1:169911396-169912013	SK-N-SH	brain:	n/a	n/a
47	GATA3	chr1:169918154-169918674	SK-N-SH	brain:	n/a	n/a
48	GATA3	chr1:169911256-169912162	MCF-7	breast:	n/a	n/a
49	GATA3	chr1:169903082-169904171	SK-N-SH	brain:	n/a	n/a
50	GATA3	chr1:169911405-169911989	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169898316..169900651-chr1:169903000..169904751,2	K562	blood:
2	chr1:169887846..169894353-chr1:169898169..169903456,7	K562	blood:
3	chr1:169894940..169897093-chr1:169912669..169915603,2	MCF-7	breast:
4	chr1:169913226..169915577-chr1:169917390..169920061,2	MCF-7	breast:
5	chr1:169906887..169908799-chr1:169914040..169915551,2	MCF-7	breast:
6	chr1:169906887..169908799-chr1:169914040..169915551,2	MCF-7	breast:
7	chr1:169860365..169863802-chr1:169902105..169905662,4	MCF-7	breast:
8	chr1:169898316..169900651-chr1:169903000..169904751,2	K562	blood:
9	chr1:169915601..169917304-chr1:169919424..169921809,3	MCF-7	breast:
10	chr1:169909516..169911412-chr20:55839152..55841163,2	MCF-7	breast:
11	chr1:169907968..169909649-chr1:169910615..169913475,2	K562	blood:
12	chr1:169891530..169894353-chr1:169899147..169901987,3	K562	blood:
13	chr1:169903817..169906654-chr1:169908531..169910584,2	K562	blood:
14	chr1:169883530..169886106-chr1:169901752..169904376,3	K562	blood:
15	chr1:169927495..169930307-chr1:170507858..170509808,2	K562	blood:
16	chr1:169915601..169917304-chr1:169919424..169921809,3	MCF-7	breast:
17	chr1:169863023..169865011-chr1:169913232..169916470,3	MCF-7	breast:
18	chr1:169907968..169909649-chr1:169910615..169913475,2	K562	blood:
19	chr1:169904469..169905208-chr1:169979740..169980542,2	MCF-7	breast:
20	chr1:169909334..169912008-chr1:170041825..170044429,2	MCF-7	breast:
21	chr1:169858457..169860973-chr1:169907396..169909921,2	MCF-7	breast:
22	chr1:169913226..169915577-chr1:169917390..169920061,2	MCF-7	breast:
23	chr1:169903817..169906654-chr1:169908531..169910584,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCYL3-1	chr1:169927085-169927387	NONHSAT007483

Variant related genes	Relation type
RN7SL269P	TF binding region
ENSG00000000457	chromatin interactions
ENSG00000075945	chromatin interactions
ENSG00000101144	chromatin interactions
ENSG00000120370	chromatin interactions

Extended variants
information (count: 983 )
Associated
traits (count: 95 )

Variant overlapped rSNPs/rCNVs (count:983 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs648576	chr1:169899427-169899428	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs12083317	chr1:169899430-169899431	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs532606319	chr1:169899580-169899581	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs375843462	chr1:169899589-169899590	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs565733491	chr1:169899634-169899635	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs563092543	chr1:169899700-169899701	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs370206690	chr1:169899724-169899725	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs548847926	chr1:169899732-169899733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs567480725	chr1:169899734-169899735	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs373096765	chr1:169899829-169899830	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs186183969	chr1:169899862-169899863	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs556288177	chr1:169899904-169899905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs571261544	chr1:169899976-169899977	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs538677849	chr1:169900030-169900031	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs145097201	chr1:169900040-169900041	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs553852450	chr1:169900046-169900047	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs75154793	chr1:169900054-169900055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs374519665	chr1:169900056-169900057	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs553631296	chr1:169900073-169900074	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs553209	chr1:169900113-169900114	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs543379263	chr1:169900120-169900121	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs188938510	chr1:169900263-169900264	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs61806080	chr1:169900288-169900289	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs143129589	chr1:169900309-169900310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs543671763	chr1:169900322-169900323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs2806391	chr1:169900336-169900337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs144752555	chr1:169900340-169900341	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs532503361	chr1:169900341-169900342	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs541116473	chr1:169900427-169900428	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs559355804	chr1:169900454-169900455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs530014155	chr1:169900455-169900456	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs548150442	chr1:169900532-169900533	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs181928913	chr1:169900618-169900619	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs531592550	chr1:169900635-169900636	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs549710619	chr1:169900664-169900665	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs664598	chr1:169900679-169900680	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
37	rs579553	chr1:169900697-169900698	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs148502767	chr1:169900701-169900702	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs114808934	chr1:169900724-169900725	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs531108818	chr1:169900806-169900807	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs186584268	chr1:169900828-169900829	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs554515901	chr1:169900864-169900865	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs61806081	chr1:169900927-169900928	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs16862766	chr1:169900932-169900933	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs150586814	chr1:169900946-169900947	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs192251207	chr1:169900969-169900970	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs76069598	chr1:169901032-169901033	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs541153271	chr1:169901056-169901057	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs559441261	chr1:169901068-169901069	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs574556028	chr1:169901174-169901175	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:95)

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
Glioblastoma multiforme	21080181	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
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
Breast cancer	21509527	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
Malignant peripheral nerve sheath tumor	18522746	CNVD
Williams-beuren syndrome	16971481	CNVD
Developmental delay	21147756	CNVD
Burkitt''s lymphoma	20823134	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Lung cancer	18438408	CNVD
Cancer	20164920	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:329 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169876200-169903600	Weak transcription	Aorta	Aorta
2	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:169881400-169901000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:169884200-169913000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:169884600-169900600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:169884600-169900600	Weak transcription	NHDF-Ad	bronchial
7	chr1:169885200-169900800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:169885400-169913200	Weak transcription	Ovary	ovary
9	chr1:169885600-169903200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:169886400-169913000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:169886600-169915600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:169887000-169911400	Weak transcription	Left Ventricle	heart
13	chr1:169888800-169900600	Weak transcription	Fetal Stomach	stomach
14	chr1:169889600-169900600	Weak transcription	Fetal Lung	lung
15	chr1:169890800-169906200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:169891000-169911400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:169891000-169913200	Weak transcription	Adipose Nuclei	Adipose
18	chr1:169894200-169903400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:169895600-169900600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:169895600-169901000	Weak transcription	Fetal Heart	heart
21	chr1:169898400-169900800	Weak transcription	Fetal Kidney	kidney
22	chr1:169899200-169900600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:169899200-169911400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:169900600-169900800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:169900600-169901000	Enhancers	Stomach Mucosa	stomach
26	chr1:169900600-169901400	Enhancers	Fetal Lung	lung
27	chr1:169900600-169901400	Enhancers	Fetal Stomach	stomach
28	chr1:169900600-169901600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:169900600-169901600	Enhancers	NHLF	lung
30	chr1:169900600-169901600	Enhancers	Osteobl	bone
31	chr1:169900600-169901800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:169900600-169901800	Enhancers	NHDF-Ad	bronchial
33	chr1:169900600-169902000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:169900800-169901200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:169900800-169901400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:169900800-169901400	Enhancers	Colon Smooth Muscle	Colon
37	chr1:169900800-169901400	Enhancers	Fetal Kidney	kidney
38	chr1:169900800-169901800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:169901000-169901400	Enhancers	Fetal Heart	heart
40	chr1:169901000-169901400	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr1:169901000-169901400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr1:169901000-169901600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:169901000-169901600	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr1:169901200-169901400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:169901200-169901400	Enhancers	Hela-S3	cervix
46	chr1:169901400-169902600	Weak transcription	Hela-S3	cervix
47	chr1:169901400-169903200	Weak transcription	Fetal Heart	heart
48	chr1:169901400-169903200	Weak transcription	Fetal Kidney	kidney
49	chr1:169901400-169903200	Weak transcription	Fetal Lung	lung
50	chr1:169901400-169903600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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