Variant report

Variant	esv10559
Chromosome Location	chr19:42547869-42553974
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:42547780-42547930	GM12865	blood:	n/a	n/a
2	EP300	chr19:42553221-42553222	K562	blood:	n/a	n/a
3	HCFC1	chr19:42553369-42553465	K562	blood:	n/a	n/a
4	IRF1	chr19:42553187-42553622	K562	blood:	n/a	chr19:42553364-42553385
5	IRF1	chr19:42552315-42552369	K562	blood:	n/a	n/a
6	IRF1	chr19:42553096-42553784	K562	blood:	n/a	chr19:42553364-42553385
7	IRF1	chr19:42552941-42553832	K562	blood:	n/a	chr19:42553364-42553385
8	JUND	chr19:42553263-42553451	K562	blood:	n/a	n/a
9	SRF	chr19:42553025-42553602	MCF-7	breast:	n/a	n/a
10	TBL1XR1	chr19:42553306-42553512	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:42550298-42550348	HepG2	liver:	n/a
2	chr19:42550298-42550348	SK-N-SH_RA	brain:	n/a
3	chr19:42550298-42550348	HCT-116	colon:	n/a
4	chr19:42550298-42550348	Hela-S3	cervix:	n/a
5	chr19:42550298-42550348	NB4	blood:	n/a
6	chr19:42550298-42550348	ProgFib	skin:	n/a
7	chr19:42550298-42550348	HUVEC	blood vessel:	n/a
8	chr19:42550298-42550348	BE2_C	brain:	n/a
9	chr19:42550298-42550348	HIPEpiC	eye:	n/a
10	chr19:42550298-42550348	GM06990	blood:	n/a
11	chr19:42550298-42550348	HAEpiC	amniotic membrane:	n/a
12	chr19:42550298-42550348	PFSK-1	brain:	n/a
13	chr19:42550298-42550348	GM19239	blood:	n/a
14	chr19:42550298-42550348	MCF-7	breast:	n/a
15	chr19:42550298-42550348	T-47D	breast:	n/a
16	chr19:42550298-42550348	HPAEpiC	pulmonary alveolar:	n/a
17	chr19:42550298-42550348	H1-hESC	embryonic stem cell:	embryo
18	chr19:42550298-42550348	AG04450	lung:	fetal
19	chr19:42550298-42550348	IMR90	lung:	fetal
20	chr19:42550298-42550348	Hepatocyte	liver:	n/a
21	chr19:42550298-42550348	Caco-2	colon:	n/a
22	chr19:42550298-42550348	RPTEC	kidney:	n/a
23	chr19:42550298-42550348	SK-N-SH	brain:	n/a
24	chr19:42550298-42550348	HL-60	blood:	n/a
25	chr19:42550298-42550348	MCF10A-Er-Src	breast:	n/a
26	chr19:42550298-42550348	SK-N-MC	brain:	n/a
27	chr19:42550298-42550348	CMK	blood:	n/a
28	chr19:42550298-42550348	HMEC	breast:	n/a
29	chr19:42550298-42550348	NHBE	bronchial:	n/a
30	chr19:42550298-42550348	HEK293	kidney:	embryo
31	chr19:42550298-42550348	A549	lung:	n/a
32	chr19:42550298-42550348	SAEC	small airway:	n/a
33	chr19:42550298-42550348	NHDF-neo	bronchial:	n/a
34	chr19:42550298-42550348	SKMC	muscle:	n/a
35	chr19:42550298-42550348	HNPCEpiC	eye:	n/a
36	chr19:42550298-42550348	HRPEpiC	eye:	n/a
37	chr19:42550298-42550348	HCF	heart:	n/a
38	chr19:42550298-42550348	AG09309	skin:	n/a
39	chr19:42550298-42550348	ECC-1	luminal epithelium:	n/a
40	chr19:42550298-42550348	AG10803	skin:	n/a
41	chr19:42550298-42550348	HCPEpiC	choroid plexus:	n/a
42	chr19:42550298-42550348	GM12891	blood:	n/a
43	chr19:42550298-42550348	HRCEpiC	kidney:	n/a
44	chr19:42550298-42550348	LNCaP	prostate:	n/a
45	chr19:42550298-42550348	U87	brain:	n/a
46	chr19:42550298-42550348	BJ	skin:	n/a
47	chr19:42550298-42550348	HRE	kidney:	n/a
48	chr19:42550298-42550348	NT2-D1	testis:	n/a
49	chr19:42550298-42550348	AG04449	skin:	fetal
50	chr19:42550298-42550348	PANC-1	pancreas:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42552423..42554392-chr19:42592510..42594306,2	K562	blood:
2	chr19:42460580..42464413-chr19:42553876..42556925,4	MCF-7	breast:
3	chr19:42553947..42555920-chr19:42562291..42564122,2	K562	blood:
4	chr19:42550327..42559850-chr19:42577425..42584775,14	MCF-7	breast:
5	chr19:42552329..42558489-chr19:42577257..42581732,10	MCF-7	breast:
6	chr19:42549668..42552954-chr19:42572953..42575417,3	K562	blood:
7	chr19:42547674..42551178-chr19:42553478..42557347,4	K562	blood:
8	chr19:42547674..42551178-chr19:42553478..42557347,4	K562	blood:
9	chr19:42553625..42555151-chr19:42564770..42567524,2	K562	blood:
10	chr19:42544185..42546473-chr19:42550888..42553041,2	K562	blood:
11	chr19:42544185..42547445-chr19:42550888..42553755,3	K562	blood:

No data

Variant related genes	Relation type
GRIK5	TF binding region
GRIK5	CpG island
ENSG00000105737	chromatin interactions
ENSG00000105404	chromatin interactions
ENSG00000105732	chromatin interactions
ENSG00000268525	chromatin interactions

Extended variants
information (count: 174 )
Associated
traits (count: 63 )

Variant overlapped rSNPs/rCNVs (count:174 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs568823093	chr19:42547916-42547917	Weak transcription Strong transcription Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs113161159	chr19:42547988-42547989	Weak transcription Strong transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs373844499	chr19:42548073-42548074	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs111754684	chr19:42548089-42548090	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs181678457	chr19:42548091-42548092	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs555186514	chr19:42548160-42548161	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs185809047	chr19:42548170-42548171	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs537444934	chr19:42548190-42548191	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs556083323	chr19:42548193-42548194	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs117944582	chr19:42548278-42548279	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs572818769	chr19:42548329-42548330	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs34356635	chr19:42548353-42548354	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs546564564	chr19:42548389-42548390	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs539826154	chr19:42548404-42548405	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs558655644	chr19:42548405-42548406	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs573508514	chr19:42548437-42548438	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs561525090	chr19:42548445-42548446	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs540796311	chr19:42548448-42548449	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs140253099	chr19:42548455-42548456	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs35533644	chr19:42548512-42548513	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs529350013	chr19:42548524-42548525	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs544371994	chr19:42548526-42548527	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs562591130	chr19:42548527-42548528	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs142057929	chr19:42548559-42548560	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs190220903	chr19:42548574-42548575	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs151129729	chr19:42548584-42548585	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs559981724	chr19:42548802-42548803	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs11669490	chr19:42548909-42548910	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs576857309	chr19:42548931-42548932	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs527514671	chr19:42548937-42548938	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs549113092	chr19:42548944-42548945	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs141087577	chr19:42548963-42548964	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs368755211	chr19:42549005-42549006	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs181263576	chr19:42549033-42549034	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs549606270	chr19:42549038-42549039	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs544453037	chr19:42549039-42549040	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs74986551	chr19:42549164-42549165	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs562750212	chr19:42549177-42549178	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs538620332	chr19:42549197-42549198	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs558513655	chr19:42549234-42549235	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs573533927	chr19:42549265-42549266	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs534140665	chr19:42549329-42549330	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs374727509	chr19:42549332-42549333	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs574150799	chr19:42549413-42549414	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs544721766	chr19:42549419-42549420	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs562627291	chr19:42549520-42549521	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs577630881	chr19:42549596-42549597	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs544973803	chr19:42549597-42549598	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs530195087	chr19:42549602-42549603	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs560019448	chr19:42549740-42549741	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:63)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21858162	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Invasive pancreatic ductal carcinoma	18765526	CNVD
Rhabdomyosarcoma	16790082	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Gastric cancer	18160780	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Renal cell carcinoma	18765545	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Genital abnormality	22378287	CNVD
Hypospadia	22378287	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Astrocytoma	22246337	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:191 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42528400-42553000	Weak transcription	Spleen	Spleen
2	chr19:42535600-42555200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr19:42537000-42553200	Weak transcription	Colon Smooth Muscle	Colon
4	chr19:42537000-42557200	Weak transcription	Fetal Kidney	kidney
5	chr19:42537200-42558600	Weak transcription	Brain Hippocampus Middle	brain
6	chr19:42539000-42556400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:42539400-42570200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:42539400-42572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:42540400-42572600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:42540600-42550800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:42540600-42551000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr19:42540600-42551600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:42540800-42551000	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr19:42540800-42551800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr19:42541800-42551200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:42542600-42553400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:42542800-42556400	Weak transcription	Right Ventricle	heart
18	chr19:42543400-42556400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr19:42543800-42550200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:42544200-42552200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:42544200-42553600	Weak transcription	Pancreas	Pancrea
22	chr19:42544600-42550400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr19:42544800-42553400	Weak transcription	Gastric	stomach
24	chr19:42545200-42550800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:42546000-42556000	Weak transcription	Fetal Muscle Leg	muscle
26	chr19:42546600-42549200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:42546600-42549200	Weak transcription	Brain Angular Gyrus	brain
28	chr19:42546600-42549600	Enhancers	Fetal Brain Male	brain
29	chr19:42546600-42550200	Weak transcription	Brain Anterior Caudate	brain
30	chr19:42546600-42556800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:42546600-42557600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr19:42546600-42559000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:42547000-42549200	Weak transcription	Brain Germinal Matrix	brain
34	chr19:42547000-42549400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:42547000-42556800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:42547200-42548000	Active TSS	Fetal Brain Female	brain
37	chr19:42547200-42548600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:42547200-42548600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:42547200-42548600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr19:42547200-42549200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:42547200-42549200	Weak transcription	Aorta	Aorta
42	chr19:42547200-42555800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:42547400-42548800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:42547600-42549200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr19:42547800-42548200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:42547800-42550400	Strong transcription	Fetal Stomach	stomach
47	chr19:42548000-42548200	Enhancers	Fetal Brain Female	brain
48	chr19:42548200-42548400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:42548200-42549000	Weak transcription	Fetal Brain Female	brain
50	chr19:42548400-42549000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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