Variant report

Variant	nsv1011557
Chromosome Location	chr1:179426390-179459460
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:71)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:71 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr1:179445580-179446074	HCT-116	colon:	n/a	n/a
2	CBX3	chr1:179445638-179446037	K562	blood:	n/a	n/a
3	CBX3	chr1:179445664-179446046	HCT-116	colon:	n/a	n/a
4	CBX3	chr1:179445633-179446049	K562	blood:	n/a	n/a
5	CEBPB	chr1:179451118-179451130	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:179454141-179454154	MCF-7	breast:	n/a	n/a
7	CTCF	chr1:179447040-179447190	HEK293	kidney:	n/a	n/a
8	CTCF	chr1:179454165-179454208	MCF-7	breast:	n/a	n/a
9	CTCF	chr1:179442599-179442628	GM10266	blood:	n/a	n/a
10	CTCF	chr1:179443021-179443099	GM13976	blood:	n/a	n/a
11	CTCF	chr1:179441074-179441115	GM10248	blood:	n/a	n/a
12	CTCF	chr1:179427249-179427289	GM13976	blood:	n/a	n/a
13	FAM48A	chr1:179435979-179436122	GM12878	blood:	n/a	n/a
14	FOXA1	chr1:179454199-179454469	T-47D	breast:	n/a	n/a
15	FOXA2	chr1:179434780-179435176	A549	lung:	n/a	n/a
16	GATA2	chr1:179451274-179451404	SH-SY5Y	brain:	n/a	n/a
17	JUN	chr1:179445715-179445933	K562	blood:	n/a	n/a
18	KAP1	chr1:179445677-179445989	U2OS	brain:	n/a	n/a
19	KAP1	chr1:179456091-179456217	U2OS	brain:	n/a	n/a
20	KAP1	chr1:179445177-179446331	K562	blood:	n/a	n/a
21	KAP1	chr1:179447487-179447873	HEK293	kidney:	n/a	n/a
22	KAP1	chr1:179443976-179444208	HEK293	kidney:	n/a	n/a
23	MAFF	chr1:179445291-179445411	HepG2	liver:	n/a	n/a
24	MAFK	chr1:179445302-179445494	HepG2	liver:	n/a	n/a
25	MAFK	chr1:179445302-179445480	HepG2	liver:	n/a	n/a
26	MAFK	chr1:179452256-179452531	HepG2	liver:	n/a	n/a
27	MAZ	chr1:179437312-179437337	HepG2	liver:	n/a	n/a
28	MYC	chr1:179453888-179453972	MCF-7	breast:	n/a	n/a
29	MYC	chr1:179454229-179454294	MCF-7	breast:	n/a	n/a
30	MYC	chr1:179437749-179437791	H1-hESC	embryonic stem cell:	n/a	n/a
31	MYC	chr1:179454232-179454262	MCF-7	breast:	n/a	n/a
32	MYC	chr1:179453846-179453887	MCF-7	breast:	n/a	n/a
33	MYC	chr1:179453761-179453785	MCF-7	breast:	n/a	n/a
34	MYC	chr1:179453789-179454367	MCF-7	breast:	n/a	n/a
35	MYC	chr1:179454269-179454270	MCF-7	breast:	n/a	n/a
36	MYC	chr1:179454031-179454312	MCF-7	breast:	n/a	n/a
37	PAX5	chr1:179453602-179454021	GM12878	blood:	n/a	n/a
38	PAX5	chr1:179453618-179453951	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:179447391-179447448	Gliobla	brain:	n/a	n/a
40	POLR2A	chr1:179454106-179454360	MCF-7	breast:	n/a	n/a
41	POLR2A	chr1:179454273-179454345	A549	lung:	n/a	n/a
42	POLR2A	chr1:179447257-179447265	A549	lung:	n/a	n/a
43	POLR2A	chr1:179453770-179454076	MCF-7	breast:	n/a	n/a
44	POLR2A	chr1:179453690-179454304	MCF-7	breast:	n/a	n/a
45	POLR2A	chr1:179453978-179454268	A549	lung:	n/a	n/a
46	POLR2A	chr1:179454306-179454377	MCF-7	breast:	n/a	n/a
47	POLR2A	chr1:179453821-179453906	A549	lung:	n/a	n/a
48	POLR2A	chr1:179429768-179429920	H1-hESC	embryonic stem cell:	n/a	n/a
49	REST	chr1:179429769-179429902	H1-hESC	embryonic stem cell:	n/a	n/a
50	RFX5	chr1:179440344-179440359	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179450571..179452564-chr1:179459735..179462060,2	K562	blood:
2	chr1:179420955..179423707-chr1:179426882..179428656,2	K562	blood:
3	chr1:179445378..179447823-chr1:179449930..179453030,3	MCF-7	breast:
4	chr1:179445378..179447823-chr1:179449930..179453030,3	MCF-7	breast:
5	chr1:179452715..179454955-chr1:179456900..179459797,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPHS2-4	chr1:179426715-179426908	NONHSAT007862
2	lnc-NPHS2-4	chr1:179426230-179426567	NONHSAT007862

No data

Variant related genes	Relation type
ENSG00000269064	TF binding region
HNRNPA1P54	TF binding region
AXDND1	TF binding region
ENSG00000162779	chromatin interactions
ENSG00000269064	chromatin interactions
SATB2	miRNA target sites
PLS3	miRNA target sites

Extended variants
information (count: 367 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:367 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12740455	chr1:179426390-179426391	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs566775403	chr1:179426458-179426459	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs184150662	chr1:179426475-179426476	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs549385742	chr1:179426476-179426477	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs575585865	chr1:179426506-179426507	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs538342360	chr1:179426507-179426508	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs557706825	chr1:179426510-179426511	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs74439377	chr1:179426512-179426513	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs189686407	chr1:179426513-179426514	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs181761915	chr1:179426528-179426529	Inactive region	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs573317293	chr1:179426553-179426554	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs148923797	chr1:179426730-179426731	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs573162190	chr1:179426757-179426758	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs12759446	chr1:179426774-179426775	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs74638785	chr1:179426802-179426803	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs534189510	chr1:179426830-179426831	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs10913776	chr1:179426842-179426843	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs574119008	chr1:179426854-179426855	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs573214155	chr1:179429717-179429718	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs61826007	chr1:179429730-179429731	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs77657180	chr1:179429737-179429738	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	mRNA abundance
22	rs78762842	chr1:179429754-179429755	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs188067120	chr1:179429764-179429765	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs191329120	chr1:179429774-179429775	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs370216971	chr1:179429798-179429799	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs527553582	chr1:179429812-179429813	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs549263923	chr1:179429820-179429821	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs374817309	chr1:179429850-179429851	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs372260553	chr1:179429872-179429873	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs533045324	chr1:179429873-179429874	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs552538629	chr1:179429886-179429887	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs565897003	chr1:179429905-179429906	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs77485551	chr1:179429918-179429919	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs145145300	chr1:179429924-179429925	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs183913675	chr1:179429927-179429928	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs149622444	chr1:179429958-179429959	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs557300973	chr1:179429964-179429965	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs373082574	chr1:179429978-179429979	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs34041685	chr1:179447015-179447016	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs564472050	chr1:179447097-179447098	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs371647323	chr1:179447103-179447104	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs374639101	chr1:179447134-179447135	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs371291160	chr1:179447164-179447165	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs548771977	chr1:179447176-179447177	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs548898483	chr1:179447198-179447199	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs72721234	chr1:179447218-179447219	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs34878773	chr1:179447246-179447247	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs542547126	chr1:179447252-179447253	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs144071029	chr1:179447257-179447258	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs188075056	chr1:179447259-179447260	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:87)

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
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
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
Neuroblastoma	18923191	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Glioblastoma multiforme	17369134	CNVD
Cancer	17440070	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21611746	CNVD
Breast cancer	16397240	CNVD
Mental retardation	17847001	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	23248035	CNVD
Metanephric adenoma	20802469	CNVD

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179447000-179448000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:179447000-179448600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:179448600-179449400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:179453600-179454000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:179454000-179454400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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