Variant report

Variant	nsv946524
Chromosome Location	chr1:179558860-179559970
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:179558615-179559058	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr1:179558469-179559081	H1-neurons	neurons:	n/a	n/a
3	REST	chr1:179558504-179559033	H1-neurons	neurons:	n/a	n/a
4	REST	chr1:179559524-179559871	H1-neurons	neurons:	n/a	chr1:179559808-179559826

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:179558954-179559004	Hepatocyte	liver:	n/a
2	chr1:179558954-179559004	Jurkat	blood:	n/a
3	chr1:179558954-179559004	PFSK-1	brain:	n/a
4	chr1:179558954-179559004	NHBE	bronchial:	n/a
5	chr1:179558954-179559004	HMEC	breast:	n/a
6	chr1:179558954-179559004	HAEpiC	amniotic membrane:	n/a
7	chr1:179558954-179559004	SK-N-MC	brain:	n/a
8	chr1:179558954-179559004	A549	lung:	n/a
9	chr1:179558954-179559004	HIPEpiC	eye:	n/a
10	chr1:179558954-179559004	AG09319	gingival:	n/a
11	chr1:179558954-179559004	HCT-116	colon:	n/a
12	chr1:179558954-179559004	NH-A	brain:	n/a
13	chr1:179558954-179559004	H1-hESC	embryonic stem cell:	embryo
14	chr1:179558954-179559004	NB4	blood:	n/a
15	chr1:179558954-179559004	U87	brain:	n/a
16	chr1:179558954-179559004	AG10803	skin:	n/a
17	chr1:179558954-179559004	RPTEC	kidney:	n/a
18	chr1:179558954-179559004	GM06990	blood:	n/a
19	chr1:179558954-179559004	ECC-1	luminal epithelium:	n/a
20	chr1:179558954-179559004	K562	blood:	n/a
21	chr1:179558954-179559004	HNPCEpiC	eye:	n/a
22	chr1:179558954-179559004	HRCEpiC	kidney:	n/a
23	chr1:179558954-179559004	HL-60	blood:	n/a
24	chr1:179558954-179559004	GM19239	blood:	n/a
25	chr1:179558954-179559004	ovcar-3	ovarian:	n/a
26	chr1:179558954-179559004	Caco-2	colon:	n/a
27	chr1:179558954-179559004	BE2_C	brain:	n/a
28	chr1:179558954-179559004	PrEC	prostate:	n/a
29	chr1:179558954-179559004	LNCaP	prostate:	n/a
30	chr1:179558954-179559004	SAEC	small airway:	n/a
31	chr1:179558954-179559004	AG09309	skin:	n/a
32	chr1:179558954-179559004	GM12892	blood:	n/a
33	chr1:179558954-179559004	MCF10A-Er-Src	breast:	n/a
34	chr1:179558954-179559004	HCF	heart:	n/a
35	chr1:179558954-179559004	HCPEpiC	choroid plexus:	n/a
36	chr1:179558954-179559004	HepG2	liver:	n/a
37	chr1:179558954-179559004	BJ	skin:	n/a
38	chr1:179558954-179559004	SK-N-SH	brain:	n/a
39	chr1:179558954-179559004	NHDF-neo	bronchial:	n/a
40	chr1:179558954-179559004	HEEpiC	esophagus:	n/a
41	chr1:179558954-179559004	ProgFib	skin:	n/a
42	chr1:179558954-179559004	T-47D	breast:	n/a
43	chr1:179558954-179559004	HEK293	kidney:	embryo
44	chr1:179558954-179559004	SKMC	muscle:	n/a
45	chr1:179558954-179559004	CMK	blood:	n/a
46	chr1:179558954-179559004	GM12878	blood:	n/a
47	chr1:179558954-179559004	HRPEpiC	eye:	n/a
48	chr1:179558954-179559004	PANC-1	pancreas:	n/a
49	chr1:179558954-179559004	AoSMC	blood vessel:	n/a
50	chr1:179558954-179559004	HCM	heart:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179553040..179558877-chr1:179559940..179564416,7	MCF-7	breast:
2	chr1:179553040..179558877-chr1:179559940..179564416,7	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDRD5-1	chr1:179559507-179560440	ENSG00000261060.1
2	lnc-NPHS2-2	chr1:179559893-179559942	NONHSAT007869
3	lnc-NPHS2-2	chr1:179558479-179559134	NONHSAT007869

No data

Variant related genes	Relation type
ENSG00000261060	TF binding region
TDRD5	TF binding region
ENSG00000261060	CpG island
TDRD5	CpG island
ENSG00000227141	chromatin interactions
ENSG00000162782	chromatin interactions

Extended variants
information (count: 35 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553463191	chr1:179558902-179558903	Weak transcription	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
2	rs141675295	chr1:179558962-179558963	Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	Overlapped CNVs	n/a
3	rs374255410	chr1:179558999-179559000	Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs555400991	chr1:179559054-179559055	Weak transcription	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs575479261	chr1:179559136-179559137	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs117954289	chr1:179559166-179559167	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs12405014	chr1:179559322-179559323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs557350851	chr1:179559354-179559355	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs574957749	chr1:179559367-179559368	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs577169191	chr1:179559427-179559428	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs539946521	chr1:179559453-179559454	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs201283871	chr1:179559455-179559456	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs4652417	chr1:179559456-179559457	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs528708900	chr1:179559460-179559461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs138582336	chr1:179559508-179559509	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs562109975	chr1:179559535-179559536	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs531255786	chr1:179559547-179559548	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs551250686	chr1:179559574-179559575	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs111620316	chr1:179559589-179559590	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs570869083	chr1:179559620-179559621	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs10753199	chr1:179559632-179559633	Weak transcription	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs547162743	chr1:179559644-179559645	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs566934967	chr1:179559711-179559712	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs535323963	chr1:179559749-179559750	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs555552326	chr1:179559750-179559751	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs368367196	chr1:179559790-179559791	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs568928562	chr1:179559798-179559799	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs114862051	chr1:179559802-179559803	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs557587827	chr1:179559842-179559843	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs73035949	chr1:179559856-179559857	Weak transcription	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs539823394	chr1:179559873-179559874	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs553622738	chr1:179559896-179559897	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs138391621	chr1:179559967-179559968	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs200309087	chr1:179559969-179559970	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs398103412	chr1:179559970-179559971	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:88)

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
Pancreatic cancer	17952125	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179556000-179560600	Weak transcription	Right Atrium	heart
2	chr1:179558200-179560600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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