Variant report

Variant	nsv593060
Chromosome Location	chr3:195635686-195636469
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	BHLHE40	chr3:195635888-195636019	K562	blood:	n/a	chr3:195635932-195635948
2	BHLHE40	chr3:195636256-195636822	GM12878	blood:	n/a	chr3:195636296-195636312 chr3:195636262-195636278
3	CCNT2	chr3:195634640-195636955	K562	blood:	n/a	chr3:195636046-195636055 chr3:195636663-195636672
4	CHD1	chr3:195636239-195636429	GM12878	blood:	n/a	n/a
5	CHD2	chr3:195635771-195636031	Hela-S3	cervix:	n/a	chr3:195635821-195635831
6	CTCF	chr3:195636320-195636470	GM12866	blood:	n/a	chr3:195636399-195636412
7	CTCF	chr3:195636327-195636443	IMR90	lung:	n/a	chr3:195636399-195636412
8	CTCF	chr3:195636282-195636971	GM12878	blood:	n/a	chr3:195636399-195636412
9	CTCF	chr3:195636365-195636439	NHEK	skin:	n/a	chr3:195636399-195636412
10	CTCF	chr3:195636300-195636450	GM12872	blood:	n/a	chr3:195636399-195636412
11	CTCF	chr3:195636280-195636430	AG09319	gingival:	n/a	chr3:195636399-195636412
12	CTCF	chr3:195636333-195636447	MCF-7	breast:	n/a	chr3:195636399-195636412
13	CTCF	chr3:195636280-195636430	SK-N-SH_RA	brain:	n/a	chr3:195636399-195636412
14	CTCF	chr3:195636366-195636457	GM13977	blood:	n/a	chr3:195636399-195636412
15	CTCF	chr3:195636324-195636470	GM12891	blood:	n/a	chr3:195636399-195636412
16	CTCF	chr3:195636330-195636435	MCF-7	breast:	n/a	chr3:195636399-195636412
17	CTCF	chr3:195636320-195636470	GM12874	blood:	n/a	chr3:195636399-195636412
18	CTCF	chr3:195636281-195636435	SK-N-SH_RA	brain:	n/a	chr3:195636399-195636412
19	CTCF	chr3:195636220-195636370	GM12871	blood:	n/a	n/a
20	CTCF	chr3:195636220-195636370	GM12875	blood:	n/a	n/a
21	CTCF	chr3:195636300-195636450	AG04449	skin:	n/a	chr3:195636399-195636412
22	CTCF	chr3:195636300-195636450	HMEC	breast:	n/a	chr3:195636399-195636412
23	CTCF	chr3:195636300-195636450	GM12878	blood:	n/a	chr3:195636399-195636412
24	CTCF	chr3:195636316-195636468	GM10266	blood:	n/a	chr3:195636399-195636412
25	CTCF	chr3:195636320-195636457	Fibrobl	skin:	n/a	chr3:195636399-195636412
26	CTCF	chr3:195636280-195636430	GM12875	blood:	n/a	chr3:195636399-195636412
27	CTCF	chr3:195636328-195636469	GM19240	blood:	n/a	chr3:195636399-195636412
28	CTCF	chr3:195636241-195636476	K562	blood:	n/a	chr3:195636399-195636412
29	CTCF	chr3:195636280-195636430	GM12865	blood:	n/a	chr3:195636399-195636412
30	CTCF	chr3:195636320-195636470	GM12867	blood:	n/a	chr3:195636399-195636412
31	CTCF	chr3:195636320-195636470	HUVEC	blood vessel:	n/a	chr3:195636399-195636412
32	CTCF	chr3:195636320-195636470	GM12869	blood:	n/a	chr3:195636399-195636412
33	CTCF	chr3:195636040-195636190	GM12866	blood:	n/a	n/a
34	CTCF	chr3:195636318-195636464	GM19239	blood:	n/a	chr3:195636399-195636412
35	CTCF	chr3:195636379-195636454	H1-hESC	embryonic stem cell:	n/a	chr3:195636399-195636412
36	CTCF	chr3:195636300-195636450	GM12870	blood:	n/a	chr3:195636399-195636412
37	CTCF	chr3:195636323-195636459	GM12892	blood:	n/a	chr3:195636399-195636412
38	CTCF	chr3:195636310-195636461	GM19238	blood:	n/a	chr3:195636399-195636412
39	CTCF	chr3:195636332-195636441	MCF-7	breast:	n/a	chr3:195636399-195636412
40	CTCF	chr3:195636234-195636517	K562	blood:	n/a	chr3:195636399-195636412
41	CTCF	chr3:195636328-195636426	GM10248	blood:	n/a	chr3:195636399-195636412
42	CTCF	chr3:195636320-195636470	GM12871	blood:	n/a	chr3:195636399-195636412
43	CTCF	chr3:195636320-195636470	GM12868	blood:	n/a	chr3:195636399-195636412
44	CTCF	chr3:195636349-195636462	GM13976	blood:	n/a	chr3:195636399-195636412
45	CTCF	chr3:195635560-195635710	GM12865	blood:	n/a	n/a
46	CTCF	chr3:195636300-195636450	GM12874	blood:	n/a	chr3:195636399-195636412
47	CTCF	chr3:195636320-195636470	GM12864	blood:	n/a	chr3:195636399-195636412
48	CTCF	chr3:195636340-195636347	GM13976	blood:	n/a	n/a
49	CTCF	chr3:195636300-195636450	SK-N-SH_RA	brain:	n/a	chr3:195636399-195636412
50	CTCF	chr3:195636297-195636445	HepG2	liver:	n/a	chr3:195636399-195636412

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:195635643-195635693	SKMC	muscle:	n/a
2	chr3:195635643-195635693	HMEC	breast:	n/a
3	chr3:195636414-195636464	GM06990	blood:	n/a
4	chr3:195635643-195635693	GM06990	blood:	n/a
5	chr3:195635643-195635693	HPAEpiC	pulmonary alveolar:	n/a
6	chr3:195635643-195635693	RPTEC	kidney:	n/a
7	chr3:195635643-195635693	ECC-1	luminal epithelium:	n/a
8	chr3:195636243-195636293	IMR90	lung:	fetal
9	chr3:195635643-195635693	CMK	blood:	n/a
10	chr3:195636243-195636293	LNCaP	prostate:	n/a
11	chr3:195636414-195636464	SK-N-SH_RA	brain:	n/a
12	chr3:195635643-195635693	IMR90	lung:	fetal
13	chr3:195636243-195636293	HPAEpiC	pulmonary alveolar:	n/a
14	chr3:195636414-195636464	HCM	heart:	n/a
15	chr3:195636414-195636464	NHBE	bronchial:	n/a
16	chr3:195636414-195636464	PANC-1	pancreas:	n/a
17	chr3:195635643-195635693	GM12891	blood:	n/a
18	chr3:195636243-195636293	HCPEpiC	choroid plexus:	n/a
19	chr3:195635643-195635693	HL-60	blood:	n/a
20	chr3:195636243-195636293	NHDF-neo	bronchial:	n/a
21	chr3:195636243-195636293	GM12891	blood:	n/a
22	chr3:195636243-195636293	HRCEpiC	kidney:	n/a
23	chr3:195635643-195635693	ProgFib	skin:	n/a
24	chr3:195635643-195635693	K562	blood:	n/a
25	chr3:195636243-195636293	CMK	blood:	n/a
26	chr3:195636243-195636293	HMEC	breast:	n/a
27	chr3:195636414-195636464	PFSK-1	brain:	n/a
28	chr3:195635643-195635693	SK-N-SH	brain:	n/a
29	chr3:195636243-195636293	SK-N-MC	brain:	n/a
30	chr3:195636414-195636464	A549	lung:	n/a
31	chr3:195636414-195636464	Hepatocyte	liver:	n/a
32	chr3:195636243-195636293	H1-hESC	embryonic stem cell:	embryo
33	chr3:195636414-195636464	GM12892	blood:	n/a
34	chr3:195636243-195636293	SAEC	small airway:	n/a
35	chr3:195636414-195636464	Hela-S3	cervix:	n/a
36	chr3:195636243-195636293	RPTEC	kidney:	n/a
37	chr3:195636243-195636293	AG04450	lung:	fetal
38	chr3:195636414-195636464	GM12878	blood:	n/a
39	chr3:195636243-195636293	HIPEpiC	eye:	n/a
40	chr3:195636243-195636293	K562	blood:	n/a
41	chr3:195636414-195636464	AG09309	skin:	n/a
42	chr3:195635643-195635693	AG10803	skin:	n/a
43	chr3:195636243-195636293	MCF10A-Er-Src	breast:	n/a
44	chr3:195636414-195636464	ECC-1	luminal epithelium:	n/a
45	chr3:195636414-195636464	HAEpiC	amniotic membrane:	n/a
46	chr3:195636414-195636464	NHDF-neo	bronchial:	n/a
47	chr3:195636414-195636464	MCF10A-Er-Src	breast:	n/a
48	chr3:195635643-195635693	NHDF-neo	bronchial:	n/a
49	chr3:195635643-195635693	Jurkat	blood:	n/a
50	chr3:195635643-195635693	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:195634985..195639388-chr3:195640414..195643668,6	K562	blood:
2	chr3:195636011..195638279-chr3:195638767..195643547,4	K562	blood:
3	chr3:195409239..195411118-chr3:195634886..195637681,2	K562	blood:
4	chr3:195586941..195589694-chr3:195636137..195637695,2	K562	blood:
5	chr3:195635569..195638518-chr3:195807424..195810696,3	MCF-7	breast:
6	chr3:195624153..195625110-chr3:195636048..195637005,2	MCF-7	breast:
7	chr3:195620885..195622532-chr3:195635337..195638039,2	K562	blood:
8	chr3:195593794..195596645-chr3:195636219..195637951,2	MCF-7	breast:
9	chr17:57922900..57925382-chr3:195635106..195637733,2	MCF-7	breast:
10	chr3:195602309..195605964-chr3:195633937..195639111,7	MCF-7	breast:
11	chr3:195601233..195610120-chr3:195632410..195638442,11	MCF-7	breast:
12	chr3:195586183..195589245-chr3:195634778..195636892,3	MCF-7	breast:
13	chr3:195623300..195626521-chr3:195635118..195637851,4	K562	blood:

Variant related genes	Relation type
TNK2	TF binding region
ENSG00000226155	TF binding region
TNK2	CpG island
ENSG00000226155	CpG island
ENSG00000226155	chromatin interactions
ENSG00000072274	chromatin interactions
ENSG00000061938	chromatin interactions
ENSG00000201524	chromatin interactions
ENSG00000223783	chromatin interactions
ENSG00000242086	chromatin interactions
ENSG00000273009	chromatin interactions

Extended variants
information (count: 12 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs567842459	chr3:195635712-195635713	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
2	rs535045094	chr3:195635737-195635738	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
3	rs553613077	chr3:195635806-195635807	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
4	rs571694438	chr3:195635821-195635822	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
5	rs73087356	chr3:195635855-195635856	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	7 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs557505860	chr3:195635885-195635886	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
7	rs546114203	chr3:195635948-195635949	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
8	rs190221775	chr3:195635977-195635978	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
9	rs372270259	chr3:195636033-195636034	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
10	rs35990866	chr3:195636042-195636043	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
11	rs543606296	chr3:195636401-195636402	Active TSS Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
12	rs555320806	chr3:195636421-195636422	Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

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
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:172 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195632600-195637200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:195632800-195635800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr3:195632800-195635800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:195633000-195636000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:195633000-195636000	Flanking Active TSS	Dnd41	blood
6	chr3:195633200-195635800	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr3:195633200-195635800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr3:195633200-195636200	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr3:195633400-195635800	Enhancers	Fetal Brain Male	brain
10	chr3:195633400-195635800	Enhancers	Fetal Heart	heart
11	chr3:195633600-195636000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:195633600-195636000	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr3:195633600-195636000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr3:195633800-195635800	Flanking Active TSS	Placenta	Placenta
15	chr3:195634000-195636000	Flanking Active TSS	Colonic Mucosa	Colon
16	chr3:195634200-195636000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr3:195634400-195635800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:195634400-195635800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
19	chr3:195634400-195636800	Active TSS	Small Intestine	intestine
20	chr3:195634600-195635800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:195634600-195635800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
22	chr3:195634600-195637200	Active TSS	Psoas Muscle	Psoas
23	chr3:195634800-195635800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:195634800-195636800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:195635000-195635800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr3:195635000-195635800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
27	chr3:195635000-195636800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:195635000-195636800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:195635000-195636800	Active TSS	Thymus	Thymus
30	chr3:195635000-195637000	Active TSS	A549	lung
31	chr3:195635000-195637200	Active TSS	Fetal Kidney	kidney
32	chr3:195635200-195635800	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr3:195635200-195636000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:195635200-195636800	Active TSS	Primary T cells from cord blood	blood
35	chr3:195635200-195636800	Active TSS	Brain Hippocampus Middle	brain
36	chr3:195635200-195636800	Active TSS	Brain Substantia Nigra	brain
37	chr3:195635200-195637000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:195635200-195637000	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr3:195635200-195637000	Active TSS	Brain Cingulate Gyrus	brain
40	chr3:195635200-195637200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr3:195635200-195637200	Active TSS	Aorta	Aorta
42	chr3:195635400-195636000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:195635400-195636000	Active TSS	Primary monocytes fromperipheralblood	blood
44	chr3:195635400-195636000	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr3:195635400-195636800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:195635400-195636800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:195635400-195636800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:195635400-195636800	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr3:195635400-195636800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:195635400-195636800	Active TSS	Primary neutrophils fromperipheralblood	blood

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