Variant report

Variant	nsv878097
Chromosome Location	chr3:190597323-190650051
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	ARID3A	chr3:190602248-190602331	K562	blood:	n/a	n/a
2	BHLHE40	chr3:190599409-190599484	GM12878	blood:	n/a	n/a
3	CCNT2	chr3:190626181-190626314	K562	blood:	n/a	n/a
4	CEBPB	chr3:190618965-190619043	HepG2	liver:	n/a	chr3:190618972-190618983 chr3:190618973-190618982 chr3:190618971-190618984
5	CEBPB	chr3:190607200-190607388	HepG2	liver:	n/a	chr3:190607311-190607322
6	CEBPB	chr3:190612784-190612984	HepG2	liver:	n/a	chr3:190612900-190612911
7	CTCF	chr3:190602160-190602310	GM12873	blood:	n/a	chr3:190602194-190602210
8	CTCF	chr3:190602140-190602290	AoAF	blood vessel:	n/a	chr3:190602194-190602210
9	CTCF	chr3:190602140-190602290	HCM	heart:	n/a	chr3:190602194-190602210
10	CTCF	chr3:190602040-190602190	WI-38	lung:	n/a	n/a
11	CTCF	chr3:190602053-190602325	GM13977	blood:	n/a	chr3:190602194-190602210
12	CTCF	chr3:190602120-190602270	AG10803	skin:	n/a	chr3:190602194-190602210
13	CTCF	chr3:190602140-190602290	K562	blood:	n/a	chr3:190602194-190602210
14	CTCF	chr3:190601843-190602609	A549	lung:	n/a	chr3:190602194-190602210
15	CTCF	chr3:190602043-190602334	Medullo	brain:	n/a	chr3:190602194-190602210
16	CTCF	chr3:190601972-190602358	H1-hESC	embryonic stem cell:	n/a	chr3:190602194-190602210
17	CTCF	chr3:190602100-190602250	GM12874	blood:	n/a	chr3:190602194-190602210
18	CTCF	chr3:190602120-190602270	HEEpiC	esophagus:	n/a	chr3:190602194-190602210
19	CTCF	chr3:190602140-190602290	HUVEC	blood vessel:	n/a	chr3:190602194-190602210
20	CTCF	chr3:190602140-190602290	GM12866	blood:	n/a	chr3:190602194-190602210
21	CTCF	chr3:190602140-190602290	AG04450	lung:	n/a	chr3:190602194-190602210
22	CTCF	chr3:190601949-190602439	A549	lung:	n/a	chr3:190602194-190602210
23	CTCF	chr3:190602140-190602290	NHLF	lung:	n/a	chr3:190602194-190602210
24	CTCF	chr3:190602082-190602288	ProgFib	skin:	n/a	chr3:190602194-190602210
25	CTCF	chr3:190610540-190610690	HEEpiC	esophagus:	n/a	n/a
26	CTCF	chr3:190602147-190602235	MCF-7	breast:	n/a	chr3:190602194-190602210
27	CTCF	chr3:190601483-190601536	MCF-7	breast:	n/a	n/a
28	CTCF	chr3:190602087-190602290	HepG2	liver:	n/a	chr3:190602194-190602210
29	CTCF	chr3:190602084-190602308	GM20000	blood:	n/a	chr3:190602194-190602210
30	CTCF	chr3:190602036-190602258	SK-N-SH_RA	brain:	n/a	chr3:190602194-190602210
31	CTCF	chr3:190602080-190602230	GM12867	blood:	n/a	chr3:190602194-190602210
32	CTCF	chr3:190602120-190602270	AoAF	blood vessel:	n/a	chr3:190602194-190602210
33	CTCF	chr3:190602079-190602317	Kidney_OC	kidney:	n/a	chr3:190602194-190602210
34	CTCF	chr3:190602140-190602290	AG09309	skin:	n/a	chr3:190602194-190602210
35	CTCF	chr3:190604740-190604890	GM06990	blood:	n/a	n/a
36	CTCF	chr3:190601907-190602442	T-47D	breast:	n/a	chr3:190602194-190602210
37	CTCF	chr3:190602062-190602314	Hela-S3	cervix:	n/a	chr3:190602194-190602210
38	CTCF	chr3:190602140-190602290	HA-sp	spinal cord:	n/a	chr3:190602194-190602210
39	CTCF	chr3:190602140-190602290	GM06990	blood:	n/a	chr3:190602194-190602210
40	CTCF	chr3:190610562-190610745	NHEK	skin:	n/a	n/a
41	CTCF	chr3:190602100-190602250	WERI-Rb-1	eye:	n/a	chr3:190602194-190602210
42	CTCF	chr3:190601954-190602395	MCF-7	breast:	n/a	chr3:190602194-190602210
43	CTCF	chr3:190610540-190610690	HAc	cerebellar:	n/a	n/a
44	CTCF	chr3:190602120-190602270	AG04449	skin:	n/a	chr3:190602194-190602210
45	CTCF	chr3:190602020-190602170	A549	lung:	n/a	n/a
46	CTCF	chr3:190602100-190602250	RPTEC	kidney:	n/a	chr3:190602194-190602210
47	CTCF	chr3:190602040-190602190	GM12872	blood:	n/a	n/a
48	CTCF	chr3:190602062-190602317	LNCaP	prostate:	n/a	chr3:190602194-190602210
49	CTCF	chr3:190602140-190602290	HVMF	connective:	n/a	chr3:190602194-190602210
50	CTCF	chr3:190602060-190602210	HAc	cerebellar:	n/a	chr3:190602194-190602210

No.	Distal block	Cell Line	Cell type
1	chr3:190645157..190647983-chr3:190753958..190756596,2	K562	blood:
2	chr3:190418930..190419478-chr3:190601767..190602267,2	MCF-7	breast:
3	chr3:190601679..190602537-chr3:190768672..190769490,5	MCF-7	breast:
4	chr3:190601751..190602362-chr3:192162433..192162941,2	K562	blood:
5	chr12:87572443..87573395-chr3:190629682..190630453,2	MCF-7	breast:

Variant related genes	Relation type
GMNC	TF binding region

Extended variants
information (count: 340 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:340 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs546653784	chr3:190602036-190602037	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs566961159	chr3:190602053-190602054	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs9818981	chr3:190602087-190602088	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs371108862	chr3:190602117-190602118	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs549548194	chr3:190602123-190602124	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs569388320	chr3:190602141-190602142	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs74588302	chr3:190602152-190602153	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs558511586	chr3:190602193-190602194	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs577678829	chr3:190602259-190602260	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs9290957	chr3:190602301-190602302	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs553539176	chr3:190602346-190602347	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs573676191	chr3:190602347-190602348	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs542398686	chr3:190602367-190602368	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs185157800	chr3:190602376-190602377	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs188028889	chr3:190602391-190602392	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs146013675	chr3:190602403-190602404	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs564849629	chr3:190602410-190602411	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs139913570	chr3:190602453-190602454	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs192826354	chr3:190602493-190602494	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs560327803	chr3:190602511-190602512	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs191882089	chr3:190604618-190604619	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs183377065	chr3:190604709-190604710	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs187296382	chr3:190604711-190604712	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs192137623	chr3:190604720-190604721	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs375990541	chr3:190604742-190604743	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs536541257	chr3:190604746-190604747	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs183457243	chr3:190604747-190604748	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs537390131	chr3:190604758-190604759	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs556579671	chr3:190604765-190604766	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs140178455	chr3:190604822-190604823	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs545487000	chr3:190604824-190604825	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs553337001	chr3:190604840-190604841	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs575791712	chr3:190604856-190604857	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs565393902	chr3:190604912-190604913	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs199929421	chr3:190604944-190604945	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs541266695	chr3:190604955-190604956	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs79093172	chr3:190604963-190604964	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs530314542	chr3:190604968-190604969	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs550090269	chr3:190604994-190604995	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs562916986	chr3:190604998-190604999	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs531998828	chr3:190605029-190605030	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs551817192	chr3:190605060-190605061	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs74634067	chr3:190605080-190605081	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs534764012	chr3:190605088-190605089	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs34456901	chr3:190605100-190605101	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs563095678	chr3:190605128-190605129	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs9290958	chr3:190605157-190605158	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs150304053	chr3:190605164-190605165	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs532023383	chr3:190610200-190610201	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs552127576	chr3:190610230-190610231	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

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	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
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Parkinson disease	21907011	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Autism	18414403	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Lung cancer	19547694	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Cancer	20164919	CNVD
Myelofibrosis	22110671	CNVD
Optic atrophy	21457585	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-small cell lung cancer	21829676	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Esophageal cancer	20955586	CNVD
Breast cancer	16397240	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:190602000-190602600	Enhancers	Liver	Liver
2	chr3:190602200-190602400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:190604600-190605200	Enhancers	NHEK	skin
4	chr3:190610200-190610800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:190610600-190610800	Bivalent Enhancer	Esophagus	oesophagus
6	chr3:190610600-190611000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:190611000-190611200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:190627600-190627800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:190627800-190628400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:190628400-190629400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:190628600-190629200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:190628800-190629400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr3:190628800-190629600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:190629000-190629600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:190629000-190630000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:190629000-190630600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:190629200-190629600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:190629200-190629600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr3:190629400-190629600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:190630400-190630800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:190630400-190631200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:190633000-190633200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:190634400-190635400	Enhancers	Ovary	ovary
24	chr3:190644000-190644600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr3:190644400-190644800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:190645800-190646000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links