Variant report

Variant	nsv946479
Chromosome Location	chr1:165549846-165553079
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:244)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:165550106-165550709	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:165550127-165550754	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:165550197-165550565	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:165550156-165550572	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr1:165550256-165550558	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr1:165551377-165551526	MCF-7	breast:	n/a	n/a
7	MYC	chr1:165550112-165550646	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:165551363-165551426	A549	lung:	n/a	n/a
9	POLR2A	chr1:165551240-165551517	MCF-7	breast:	n/a	n/a
10	POLR2A	chr1:165551480-165551497	MCF-7	breast:	n/a	n/a
11	POLR2A	chr1:165551459-165551490	A549	lung:	n/a	n/a
12	POLR2A	chr1:165551228-165551474	MCF-7	breast:	n/a	n/a
13	STAT3	chr1:165550203-165550443	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr1:165550247-165550746	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr1:165550247-165550707	MCF10A-Er-Src	breast:	n/a	n/a

(count:244 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:165551490-165551540	A549	lung:	n/a
2	chr1:165550932-165550982	BJ	skin:	n/a
3	chr1:165551210-165551260	NB4	blood:	n/a
4	chr1:165550932-165550982	HIPEpiC	eye:	n/a
5	chr1:165551210-165551260	AG09319	gingival:	n/a
6	chr1:165551490-165551540	PrEC	prostate:	n/a
7	chr1:165551490-165551540	MCF10A-Er-Src	breast:	n/a
8	chr1:165551424-165551474	Hepatocyte	liver:	n/a
9	chr1:165551490-165551540	K562	blood:	n/a
10	chr1:165551210-165551260	MCF10A-Er-Src	breast:	n/a
11	chr1:165551424-165551474	HRPEpiC	eye:	n/a
12	chr1:165550932-165550982	T-47D	breast:	n/a
13	chr1:165550932-165550982	U87	brain:	n/a
14	chr1:165551210-165551260	LNCaP	prostate:	n/a
15	chr1:165550932-165550982	HRCEpiC	kidney:	n/a
16	chr1:165551490-165551540	NH-A	brain:	n/a
17	chr1:165551210-165551260	ovcar-3	ovarian:	n/a
18	chr1:165551490-165551540	GM12878	blood:	n/a
19	chr1:165551490-165551540	SKMC	muscle:	n/a
20	chr1:165551490-165551540	HCM	heart:	n/a
21	chr1:165550932-165550982	AG04450	lung:	fetal
22	chr1:165551210-165551260	Hela-S3	cervix:	n/a
23	chr1:165551210-165551260	BE2_C	brain:	n/a
24	chr1:165551210-165551260	Caco-2	colon:	n/a
25	chr1:165550932-165550982	HAEpiC	amniotic membrane:	n/a
26	chr1:165550932-165550982	PFSK-1	brain:	n/a
27	chr1:165551490-165551540	HRE	kidney:	n/a
28	chr1:165550932-165550982	ProgFib	skin:	n/a
29	chr1:165551490-165551540	RPTEC	kidney:	n/a
30	chr1:165551424-165551474	K562	blood:	n/a
31	chr1:165551210-165551260	SK-N-SH_RA	brain:	n/a
32	chr1:165551424-165551474	T-47D	breast:	n/a
33	chr1:165551210-165551260	NH-A	brain:	n/a
34	chr1:165551210-165551260	CMK	blood:	n/a
35	chr1:165550932-165550982	ovcar-3	ovarian:	n/a
36	chr1:165550932-165550982	NT2-D1	testis:	n/a
37	chr1:165551424-165551474	RPTEC	kidney:	n/a
38	chr1:165550932-165550982	PrEC	prostate:	n/a
39	chr1:165551490-165551540	HUVEC	blood vessel:	n/a
40	chr1:165551424-165551474	Hela-S3	cervix:	n/a
41	chr1:165551490-165551540	BJ	skin:	n/a
42	chr1:165550932-165550982	HCM	heart:	n/a
43	chr1:165551210-165551260	K562	blood:	n/a
44	chr1:165550932-165550982	HEK293	kidney:	embryo
45	chr1:165550932-165550982	ECC-1	luminal epithelium:	n/a
46	chr1:165550932-165550982	LNCaP	prostate:	n/a
47	chr1:165551210-165551260	HRCEpiC	kidney:	n/a
48	chr1:165551490-165551540	SK-N-SH_RA	brain:	n/a
49	chr1:165551210-165551260	Hepatocyte	liver:	n/a
50	chr1:165551490-165551540	GM06990	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165548827..165550594-chr1:165555598..165558121,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RXRG-1	chr1:165550764-165550815	NONHSAT007311
2	lnc-RXRG-1	chr1:165550592-165550738	NONHSAT007319

No data

Variant related genes	Relation type
ENSG00000237463	TF binding region
ENSG00000237783	TF binding region
ENSG00000237463	CpG island
ENSG00000237783	CpG island

Extended variants
information (count: 228 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:228 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs549599237	chr1:165549895-165549896	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs367732955	chr1:165549917-165549918	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs141801583	chr1:165549945-165549946	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs551669666	chr1:165550006-165550007	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs1572542	chr1:165550009-165550010	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs537075059	chr1:165550013-165550014	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs559473739	chr1:165550024-165550025	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs374827139	chr1:165550090-165550091	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs142966821	chr1:165550102-165550103	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs151123836	chr1:165550109-165550110	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs536057115	chr1:165550112-165550113	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs368027220	chr1:165550140-165550141	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs553085919	chr1:165550182-165550183	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs73027009	chr1:165550237-165550238	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs80003204	chr1:165550251-165550252	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs113141238	chr1:165550252-165550253	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs111840181	chr1:165550253-165550254	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs77889171	chr1:165550302-165550303	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs532660946	chr1:165550325-165550326	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs73027011	chr1:165550376-165550377	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs376116427	chr1:165550390-165550391	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs575291590	chr1:165550397-165550398	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs544261880	chr1:165550422-165550423	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs74118820	chr1:165550431-165550432	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs201412386	chr1:165550461-165550462	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs61800650	chr1:165550462-165550463	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs150744284	chr1:165550467-165550468	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs186339925	chr1:165550469-165550470	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs75900907	chr1:165550471-165550472	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs141109226	chr1:165550496-165550497	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs190840242	chr1:165550549-165550550	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs41267552	chr1:165550634-165550635	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs150183842	chr1:165550640-165550641	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs530803382	chr1:165550649-165550650	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs41267554	chr1:165550654-165550655	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs138725571	chr1:165550667-165550668	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs533434882	chr1:165550679-165550680	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs536710035	chr1:165550689-165550690	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs553207556	chr1:165550695-165550696	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs566646693	chr1:165550701-165550702	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs538867734	chr1:165550773-165550774	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs554895597	chr1:165550804-165550805	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs182105567	chr1:165550823-165550824	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs544179789	chr1:165550833-165550834	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs186571483	chr1:165550836-165550837	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs41267556	chr1:165550841-165550842	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs576989510	chr1:165550846-165550847	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs116383715	chr1:165550884-165550885	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs559843292	chr1:165550891-165550892	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs41267558	chr1:165550894-165550895	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Thoracic aortic aneurysm	21092924	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
Lung cancer	18438408	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
low-grade B-cell lymphoma tumor	18367492	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	22522925	CNVD
Myelofibrosis	22110671	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Williams-beuren syndrome	16971481	CNVD

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165547400-165566800	Weak transcription	Psoas Muscle	Psoas
2	chr1:165549000-165551000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:165549600-165551200	Enhancers	NHEK	skin
4	chr1:165549600-165551600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:165549600-165551600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:165549800-165551600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:165550000-165550200	Enhancers	Placenta	Placenta
8	chr1:165550200-165551400	Enhancers	HMEC	breast
9	chr1:165550400-165551000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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