Variant report

Variant	nsv877828
Chromosome Location	chr3:163671071-163747389
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:195)
CpG islands
(count:305)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:195 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr3:163722192-163722316	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr3:163742739-163742774	A549	lung:	n/a	n/a
3	CEBPB	chr3:163722123-163722274	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD2	chr3:163722101-163722388	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr3:163722086-163722401	H1-hESC	embryonic stem cell:	n/a	chr3:163722244-163722257
6	CTCF	chr3:163736500-163736650	MCF-7	breast:	n/a	n/a
7	CTCF	chr3:163674880-163675030	HL-60	blood:	n/a	n/a
8	CTCF	chr3:163722160-163722310	BE2_C	brain:	n/a	chr3:163722244-163722257
9	CTCF	chr3:163722140-163722290	HEK293	kidney:	n/a	chr3:163722244-163722257
10	CTCF	chr3:163698245-163698288	Kidney_OC	kidney:	n/a	n/a
11	CTCF	chr3:163674996-163675186	GM12878	blood:	n/a	n/a
12	CTCF	chr3:163674847-163675322	HCT-116	colon:	n/a	n/a
13	CTCF	chr3:163736420-163736570	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr3:163674993-163675126	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr3:163722146-163722360	H1-hESC	embryonic stem cell:	n/a	chr3:163722244-163722257
16	CTCF	chr3:163722154-163722352	K562	blood:	n/a	chr3:163722244-163722257
17	CTCF	chr3:163671708-163671754	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:163674980-163675130	MCF-7	breast:	n/a	n/a
19	CTCF	chr3:163729009-163729072	LNCaP	prostate:	n/a	n/a
20	CTCF	chr3:163722200-163722350	K562	blood:	n/a	chr3:163722244-163722257
21	CTCF	chr3:163736400-163736690	HCT-116	colon:	n/a	n/a
22	CTCF	chr3:163674999-163675163	MCF-7	breast:	n/a	n/a
23	CTCF	chr3:163722126-163722337	K562	blood:	n/a	chr3:163722244-163722257
24	CTCF	chr3:163698213-163698303	GM10248	blood:	n/a	n/a
25	CTCF	chr3:163674924-163675179	MCF-7	breast:	n/a	n/a
26	CTCF	chr3:163722120-163722270	GM12866	blood:	n/a	chr3:163722244-163722257
27	CTCF	chr3:163722060-163722210	HFF-Myc	foreskin:	n/a	n/a
28	CTCF	chr3:163722240-163722390	NB4	blood:	n/a	chr3:163722244-163722257
29	CTCF	chr3:163721960-163722110	GM12869	blood:	n/a	n/a
30	CTCF	chr3:163674940-163675090	HRPEpiC	eye:	n/a	n/a
31	CTCF	chr3:163674887-163675245	MCF-7	breast:	n/a	n/a
32	CTCF	chr3:163729030-163729112	GM20000	blood:	n/a	n/a
33	CTCF	chr3:163729568-163729594	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:163736429-163736549	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr3:163722140-163722290	WERI-Rb-1	eye:	n/a	chr3:163722244-163722257
36	CTCF	chr3:163674960-163675110	HCT-116	colon:	n/a	n/a
37	CTCF	chr3:163722040-163722190	HCT-116	colon:	n/a	n/a
38	CTCF	chr3:163736380-163736530	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr3:163684720-163684870	BE2_C	brain:	n/a	n/a
40	CTCF	chr3:163722178-163722338	K562	blood:	n/a	chr3:163722244-163722257
41	CTCF	chr3:163675040-163675190	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr3:163675000-163675150	MCF-7	breast:	n/a	n/a
43	CTCF	chr3:163722106-163722410	H1-hESC	embryonic stem cell:	n/a	chr3:163722244-163722257
44	CTCF	chr3:163722250-163722265	MCF-7	breast:	n/a	n/a
45	CTCF	chr3:163722220-163722370	GM12872	blood:	n/a	chr3:163722244-163722257
46	CTCF	chr3:163722192-163722314	MCF-7	breast:	n/a	chr3:163722244-163722257
47	CTCF	chr3:163722080-163722370	HCT-116	colon:	n/a	chr3:163722244-163722257
48	CTCF	chr3:163722140-163722290	GM12865	blood:	n/a	chr3:163722244-163722257
49	CTCF	chr3:163722180-163722330	Hela-S3	cervix:	n/a	chr3:163722244-163722257
50	CTCF	chr3:163706280-163706430	AG04450	lung:	n/a	n/a

(count:305 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:163722208-163722258	SKMC	muscle:	n/a
2	chr3:163722051-163722101	K562	blood:	n/a
3	chr3:163722294-163722344	HRPEpiC	eye:	n/a
4	chr3:163722294-163722344	PFSK-1	brain:	n/a
5	chr3:163722294-163722344	HMEC	breast:	n/a
6	chr3:163722208-163722258	HNPCEpiC	eye:	n/a
7	chr3:163722051-163722101	Hela-S3	cervix:	n/a
8	chr3:163719236-163719286	AG04450	lung:	fetal
9	chr3:163722208-163722258	NHBE	bronchial:	n/a
10	chr3:163722208-163722258	T-47D	breast:	n/a
11	chr3:163719236-163719286	AG04449	skin:	fetal
12	chr3:163719428-163719478	PrEC	prostate:	n/a
13	chr3:163722208-163722258	LNCaP	prostate:	n/a
14	chr3:163722208-163722258	BE2_C	brain:	n/a
15	chr3:163722208-163722258	PANC-1	pancreas:	n/a
16	chr3:163719236-163719286	Caco-2	colon:	n/a
17	chr3:163722051-163722101	HCPEpiC	choroid plexus:	n/a
18	chr3:163719236-163719286	NH-A	brain:	n/a
19	chr3:163722294-163722344	HRCEpiC	kidney:	n/a
20	chr3:163719236-163719286	ECC-1	luminal epithelium:	n/a
21	chr3:163722208-163722258	AG10803	skin:	n/a
22	chr3:163722294-163722344	GM06990	blood:	n/a
23	chr3:163719236-163719286	HepG2	liver:	n/a
24	chr3:163722051-163722101	AG04450	lung:	fetal
25	chr3:163722051-163722101	NHBE	bronchial:	n/a
26	chr3:163722208-163722258	PFSK-1	brain:	n/a
27	chr3:163722051-163722101	PrEC	prostate:	n/a
28	chr3:163722051-163722101	HNPCEpiC	eye:	n/a
29	chr3:163722051-163722101	SK-N-MC	brain:	n/a
30	chr3:163722051-163722101	SKMC	muscle:	n/a
31	chr3:163719428-163719478	GM19239	blood:	n/a
32	chr3:163722294-163722344	GM12892	blood:	n/a
33	chr3:163719428-163719478	HUVEC	blood vessel:	n/a
34	chr3:163719236-163719286	HUVEC	blood vessel:	n/a
35	chr3:163722294-163722344	HL-60	blood:	n/a
36	chr3:163719236-163719286	HMEC	breast:	n/a
37	chr3:163719428-163719478	AG04449	skin:	fetal
38	chr3:163719236-163719286	HIPEpiC	eye:	n/a
39	chr3:163722208-163722258	Hela-S3	cervix:	n/a
40	chr3:163719428-163719478	NB4	blood:	n/a
41	chr3:163722051-163722101	ECC-1	luminal epithelium:	n/a
42	chr3:163719428-163719478	Caco-2	colon:	n/a
43	chr3:163719236-163719286	HEEpiC	esophagus:	n/a
44	chr3:163719428-163719478	HEEpiC	esophagus:	n/a
45	chr3:163722208-163722258	AG09319	gingival:	n/a
46	chr3:163719236-163719286	HRCEpiC	kidney:	n/a
47	chr3:163719236-163719286	AoSMC	blood vessel:	n/a
48	chr3:163719236-163719286	HCT-116	colon:	n/a
49	chr3:163719236-163719286	GM12878	blood:	n/a
50	chr3:163722294-163722344	NB4	blood:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:163738641..163741233-chr3:163742705..163744722,2	MCF-7	breast:
2	chr3:163689823..163692046-chr3:163703767..163706359,2	K562	blood:
3	chr3:163674674..163675466-chr3:164524045..164524647,3	MCF-7	breast:
4	chr3:163738641..163741233-chr3:163742705..163744722,2	MCF-7	breast:
5	chr3:163689823..163692046-chr3:163703767..163706359,2	K562	blood:
6	chr3:163741470..163744256-chr3:163747090..163749437,2	K562	blood:
7	chr3:163676571..163679360-chr3:163699055..163700602,2	MCF-7	breast:
8	chr3:163741470..163744256-chr3:163747090..163749437,2	K562	blood:
9	chr3:163676571..163679360-chr3:163699055..163700602,2	MCF-7	breast:
10	chr3:163674728..163675758-chr3:164903457..164904093,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SI-6	chr3:163719394-163720253	NONHSAT093045

No data

Variant related genes	Relation type
ENSG00000214210	TF binding region
ENSG00000214210	CpG island

Extended variants
information (count: 1180 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:1180 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9829001	chr3:163671071-163671072	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs548878755	chr3:163671074-163671075	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs7627791	chr3:163671095-163671096	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs537009461	chr3:163671105-163671106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs62284178	chr3:163671106-163671107	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs570472921	chr3:163671108-163671109	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs539148792	chr3:163671145-163671146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs201827503	chr3:163671148-163671149	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs572677101	chr3:163671164-163671165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs535285943	chr3:163671169-163671170	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs7630165	chr3:163671174-163671175	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs374134496	chr3:163671178-163671179	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs563531438	chr3:163671202-163671203	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs577209341	chr3:163671203-163671204	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs7630237	chr3:163671228-163671229	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs561210153	chr3:163671239-163671240	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs11710022	chr3:163671259-163671260	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs528669346	chr3:163671290-163671291	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs551253872	chr3:163671319-163671320	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs188896567	chr3:163671322-163671323	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs112401967	chr3:163671330-163671331	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs9829413	chr3:163671341-163671342	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs562321337	chr3:163671355-163671356	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs193252157	chr3:163671358-163671359	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs9829526	chr3:163671367-163671368	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs550849749	chr3:163671384-163671385	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs539444989	chr3:163671388-163671389	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs184525063	chr3:163671439-163671440	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs370808372	chr3:163671442-163671443	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs566243053	chr3:163671477-163671478	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs149518015	chr3:163671493-163671494	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs555149265	chr3:163671516-163671517	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs73166457	chr3:163671540-163671541	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs537742638	chr3:163671549-163671550	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs9830106	chr3:163671569-163671570	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs577148001	chr3:163671608-163671609	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs546241640	chr3:163671677-163671678	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs73028705	chr3:163671708-163671709	ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs374158462	chr3:163671747-163671748	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs80210486	chr3:163671748-163671749	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs562256358	chr3:163671750-163671751	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs372652957	chr3:163671751-163671752	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs531166193	chr3:163671764-163671765	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs544555581	chr3:163671774-163671775	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs564820476	chr3:163671793-163671794	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs532755626	chr3:163671796-163671797	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs9830192	chr3:163671816-163671817	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs566186050	chr3:163671832-163671833	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs528954426	chr3:163671838-163671839	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs144140702	chr3:163671865-163671866	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD
Breast cancer	21364760	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Sudden cardiac death	19188705	CNVD
Mantle cell lymphoma	19029149	CNVD
Malformation	19546859	CNVD
Schizophrenia	19546859	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
epilepsy	18472482	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Myxofibrosarcoma	16751306	CNVD
Parkinson disease	21907011	CNVD
Bladder cancer	21909424	CNVD
Glioblastoma multiforme	21138945	CNVD
Cancer	20164919	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:163670800-163671200	Weak transcription	Pancreas	Pancrea
2	chr3:163671200-163671800	Enhancers	Pancreas	Pancrea
3	chr3:163671600-163671800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:163671800-163684800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:163686000-163686400	Active TSS	Gastric	stomach
6	chr3:163686200-163686600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:163719200-163719800	Enhancers	Fetal Stomach	stomach
8	chr3:163720600-163721200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:163721200-163721800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:163721800-163722000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:163722000-163722200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:163722200-163724600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:163724800-163727000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:163738600-163739200	Enhancers	Dnd41	blood
15	chr3:163739000-163739400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:163739400-163740400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:163740400-163740600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:163744200-163745800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:163745800-163749000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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