Variant report

Variant	nsv518925
Chromosome Location	chr3:196002067-196005444
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	chr3:196001448-196002117	K562	blood:	n/a	n/a
2	CEBPB	chr3:196005242-196005551	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr3:196005217-196005657	IMR90	lung:	n/a	n/a
4	CEBPB	chr3:196005095-196005585	K562	blood:	n/a	n/a
5	CTCF	chr3:196005354-196005410	Fibrobl	skin:	n/a	n/a
6	CTCF	chr3:196005320-196005470	HBMEC	blood vessel:	n/a	n/a
7	CTCF	chr3:196005334-196005429	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr3:196005320-196005470	GM12873	blood:	n/a	n/a
9	CTCF	chr3:196005180-196005330	HMEC	breast:	n/a	n/a
10	CTCF	chr3:196005360-196005510	HCPEpiC	choroid plexus:	n/a	n/a
11	ELF1	chr3:196005275-196005636	K562	blood:	n/a	chr3:196005507-196005518 chr3:196005436-196005449
12	EP300	chr3:196001409-196002169	K562	blood:	n/a	chr3:196001671-196001680
13	FOS	chr3:196005393-196005408	MCF10A-Er-Src	breast:	n/a	n/a
14	FOXA1	chr3:196005272-196005641	HepG2	liver:	n/a	n/a
15	FOXA2	chr3:196005315-196005565	HepG2	liver:	n/a	n/a
16	IRF1	chr3:196001313-196002119	K562	blood:	n/a	chr3:196001703-196001717 chr3:196001701-196001722 chr3:196001705-196001718 chr3:196001706-196001723 chr3:196001320-196001333 chr3:196001707-196001718 chr3:196001707-196001721 chr3:196001704-196001718 chr3:196001705-196001718 chr3:196001705-196001718 chr3:196001707-196001717
17	IRF1	chr3:196001381-196002202	K562	blood:	n/a	chr3:196001703-196001717 chr3:196001701-196001722 chr3:196001705-196001718 chr3:196001706-196001723 chr3:196001707-196001718 chr3:196001707-196001721 chr3:196001704-196001718 chr3:196001705-196001718 chr3:196001705-196001718 chr3:196001707-196001717
18	JUN	chr3:196002097-196002227	H1-hESC	embryonic stem cell:	n/a	n/a
19	JUN	chr3:196000889-196002463	K562	blood:	n/a	chr3:196001668-196001679 chr3:196001672-196001680 chr3:196001673-196001680
20	JUND	chr3:196002159-196002214	K562	blood:	n/a	n/a
21	NFIC	chr3:196001397-196002133	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:196005366-196005506	HepG2	liver:	n/a	n/a
23	RUNX3	chr3:196001392-196002389	GM12878	blood:	n/a	n/a
24	SPI1	chr3:196005331-196005610	HL-60	blood:	n/a	chr3:196005508-196005517 chr3:196005507-196005520 chr3:196005506-196005519
25	SPI1	chr3:196005182-196005754	HL-60	blood:	n/a	chr3:196005508-196005517 chr3:196005507-196005520 chr3:196005506-196005519
26	SPI1	chr3:196005358-196005604	K562	blood:	n/a	chr3:196005508-196005517 chr3:196005507-196005520 chr3:196005506-196005519
27	SPI1	chr3:196005331-196005624	GM12891	blood:	n/a	chr3:196005508-196005517 chr3:196005507-196005520 chr3:196005506-196005519
28	TBP	chr3:196001417-196002158	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:195971988..195973828-chr3:195999663..196002125,2	MCF-7	breast:
2	chr3:195999654..196002310-chr3:196064662..196066658,2	K562	blood:
3	chr3:196002671..196004229-chr3:196012757..196014327,2	MCF-7	breast:
4	chr3:195807261..195808984-chr3:196001816..196004147,2	K562	blood:
5	chr3:196005160..196007960-chr3:196014818..196016357,2	K562	blood:
6	chr3:196002832..196006454-chr3:196043671..196046780,4	MCF-7	breast:

Variant related genes	Relation type
PCYT1A	TF binding region
ENSG00000273331	chromatin interactions
ENSG00000145107	chromatin interactions
ENSG00000161217	chromatin interactions
ENSG00000235897	chromatin interactions
ENSG00000272741	chromatin interactions
ENSG00000213123	chromatin interactions
ENSG00000072274	chromatin interactions

Extended variants
information (count: 118 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:118 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4916421	chr3:196002067-196002068	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs367725061	chr3:196002119-196002120	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs570982255	chr3:196002203-196002204	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs151199888	chr3:196002303-196002304	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs181605167	chr3:196002305-196002306	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs4916456	chr3:196002323-196002324	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs2173600	chr3:196002355-196002356	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs184512927	chr3:196002359-196002360	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs561321086	chr3:196002372-196002373	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs573518297	chr3:196002377-196002378	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs540441253	chr3:196002382-196002383	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs145312220	chr3:196002429-196002430	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs192915181	chr3:196002499-196002500	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs560084817	chr3:196002505-196002506	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs577369514	chr3:196002522-196002523	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs570308289	chr3:196002594-196002595	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs200596797	chr3:196002612-196002613	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs544720142	chr3:196002617-196002618	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs563017678	chr3:196002630-196002631	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs189616868	chr3:196002644-196002645	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs115239468	chr3:196002684-196002685	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs147637546	chr3:196002732-196002733	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs528409175	chr3:196002744-196002745	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs12163633	chr3:196002769-196002770	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs562803827	chr3:196002782-196002783	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs546444355	chr3:196002805-196002806	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs571119166	chr3:196002836-196002837	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
28	rs538302035	chr3:196002882-196002883	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
29	rs550260079	chr3:196002907-196002908	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
30	rs568654814	chr3:196002940-196002941	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
31	rs535858057	chr3:196002950-196002951	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
32	rs75943043	chr3:196002969-196002970	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
33	rs554581006	chr3:196003000-196003001	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
34	rs573420737	chr3:196003034-196003035	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
35	rs534514613	chr3:196003052-196003053	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
36	rs573559323	chr3:196003065-196003066	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
37	rs57331814	chr3:196003068-196003069	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
38	rs374341472	chr3:196003131-196003132	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
39	rs577508318	chr3:196003194-196003195	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
40	rs186056281	chr3:196003213-196003214	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
41	rs562953550	chr3:196003223-196003224	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
42	rs112232506	chr3:196003266-196003267	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
43	rs368186979	chr3:196003282-196003283	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
44	rs189553551	chr3:196003331-196003332	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
45	rs58013524	chr3:196003360-196003361	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs528335920	chr3:196003382-196003383	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
47	rs148853831	chr3:196003409-196003410	Weak transcription Strong transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
48	rs7635355	chr3:196003422-196003423	Weak transcription Strong transcription Enhancers	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs532168542	chr3:196003455-196003456	Weak transcription Strong transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
50	rs550397238	chr3:196003468-196003469	Weak transcription Strong transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:82)

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
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD
Chronic lymphocytic leukemia	20421269	CNVD

Chromatin state (count:238 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
3	chr3:195974800-196005000	Weak transcription	Stomach Mucosa	stomach
4	chr3:195984800-196005000	Weak transcription	Fetal Heart	heart
5	chr3:195990400-196006400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:195991800-196012400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:195993000-196005200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:195995400-196005200	Weak transcription	A549	lung
9	chr3:195996200-196005200	Weak transcription	HUVEC	blood vessel
10	chr3:195996600-196006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:195996600-196012600	Weak transcription	Fetal Kidney	kidney
12	chr3:195997400-196006200	Weak transcription	HSMM	muscle
13	chr3:195997400-196006400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:195997600-196007800	Weak transcription	Small Intestine	intestine
15	chr3:195997600-196010600	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:195997800-196005000	Weak transcription	NHDF-Ad	bronchial
17	chr3:195997800-196006200	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:195998400-196005000	Weak transcription	Hela-S3	cervix
19	chr3:195999600-196002200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:195999600-196002200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr3:195999600-196002200	ZNF genes & repeats	Dnd41	blood
22	chr3:195999600-196002400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:196000000-196005000	Weak transcription	HepG2	liver
24	chr3:196000000-196005800	Weak transcription	Pancreas	Pancrea
25	chr3:196000200-196005200	Weak transcription	Psoas Muscle	Psoas
26	chr3:196000200-196006200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:196000400-196005000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:196000400-196005400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:196000400-196006400	Weak transcription	HSMMtube	muscle
30	chr3:196000600-196002200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:196000600-196004600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:196000600-196005000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:196000600-196005000	Weak transcription	Osteobl	bone
34	chr3:196000600-196005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:196000600-196006200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:196000600-196006200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:196000600-196006200	Weak transcription	Colonic Mucosa	Colon
38	chr3:196000600-196011200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:196000600-196012400	Weak transcription	Fetal Brain Female	brain
40	chr3:196000600-196012600	Weak transcription	Fetal Lung	lung
41	chr3:196000600-196012800	Weak transcription	Ovary	ovary
42	chr3:196000600-196013800	Weak transcription	Aorta	Aorta
43	chr3:196000800-196005000	Weak transcription	Adipose Nuclei	Adipose
44	chr3:196000800-196005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:196000800-196006200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:196001000-196002200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr3:196001000-196002200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr3:196001000-196005200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:196001000-196006200	Weak transcription	Brain Substantia Nigra	brain
50	chr3:196001000-196011600	Weak transcription	Thymus	Thymus

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