Variant report

Variant	nsv579628
Chromosome Location	chr19:42549934-42553804
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr19:42553221-42553222	K562	blood:	n/a	n/a
2	HCFC1	chr19:42553369-42553465	K562	blood:	n/a	n/a
3	IRF1	chr19:42552941-42553832	K562	blood:	n/a	chr19:42553364-42553385
4	IRF1	chr19:42553187-42553622	K562	blood:	n/a	chr19:42553364-42553385
5	IRF1	chr19:42553096-42553784	K562	blood:	n/a	chr19:42553364-42553385
6	IRF1	chr19:42552315-42552369	K562	blood:	n/a	n/a
7	JUND	chr19:42553263-42553451	K562	blood:	n/a	n/a
8	SRF	chr19:42553025-42553602	MCF-7	breast:	n/a	n/a
9	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	CMK	blood:	n/a
2	chr19:42550298-42550348	HEK293	kidney:	embryo
3	chr19:42550298-42550348	HepG2	liver:	n/a
4	chr19:42550298-42550348	NH-A	brain:	n/a
5	chr19:42550298-42550348	NT2-D1	testis:	n/a
6	chr19:42550298-42550348	HRE	kidney:	n/a
7	chr19:42550298-42550348	BE2_C	brain:	n/a
8	chr19:42550298-42550348	PANC-1	pancreas:	n/a
9	chr19:42550298-42550348	ProgFib	skin:	n/a
10	chr19:42550298-42550348	NB4	blood:	n/a
11	chr19:42550298-42550348	AG09309	skin:	n/a
12	chr19:42550298-42550348	Jurkat	blood:	n/a
13	chr19:42550298-42550348	HCPEpiC	choroid plexus:	n/a
14	chr19:42550298-42550348	K562	blood:	n/a
15	chr19:42550298-42550348	SK-N-SH_RA	brain:	n/a
16	chr19:42550298-42550348	ECC-1	luminal epithelium:	n/a
17	chr19:42550298-42550348	MCF10A-Er-Src	breast:	n/a
18	chr19:42550298-42550348	HEEpiC	esophagus:	n/a
19	chr19:42550298-42550348	AG09319	gingival:	n/a
20	chr19:42550298-42550348	A549	lung:	n/a
21	chr19:42550298-42550348	PFSK-1	brain:	n/a
22	chr19:42550298-42550348	Hela-S3	cervix:	n/a
23	chr19:42550298-42550348	NHBE	bronchial:	n/a
24	chr19:42550298-42550348	MCF-7	breast:	n/a
25	chr19:42550298-42550348	BJ	skin:	n/a
26	chr19:42550298-42550348	GM06990	blood:	n/a
27	chr19:42550298-42550348	PrEC	prostate:	n/a
28	chr19:42550298-42550348	Hepatocyte	liver:	n/a
29	chr19:42550298-42550348	HRCEpiC	kidney:	n/a
30	chr19:42550298-42550348	HL-60	blood:	n/a
31	chr19:42550298-42550348	T-47D	breast:	n/a
32	chr19:42550298-42550348	HCT-116	colon:	n/a
33	chr19:42550298-42550348	SK-N-SH	brain:	n/a
34	chr19:42550298-42550348	IMR90	lung:	fetal
35	chr19:42550298-42550348	HCM	heart:	n/a
36	chr19:42550298-42550348	HIPEpiC	eye:	n/a
37	chr19:42550298-42550348	AG04450	lung:	fetal
38	chr19:42550298-42550348	ovcar-3	ovarian:	n/a
39	chr19:42550298-42550348	HUVEC	blood vessel:	n/a
40	chr19:42550298-42550348	AG04449	skin:	fetal
41	chr19:42550298-42550348	RPTEC	kidney:	n/a
42	chr19:42550298-42550348	HAEpiC	amniotic membrane:	n/a
43	chr19:42550298-42550348	NHDF-neo	bronchial:	n/a
44	chr19:42550298-42550348	GM12892	blood:	n/a
45	chr19:42550298-42550348	SKMC	muscle:	n/a
46	chr19:42550298-42550348	Caco-2	colon:	n/a
47	chr19:42550298-42550348	LNCaP	prostate:	n/a
48	chr19:42550298-42550348	GM12891	blood:	n/a
49	chr19:42550298-42550348	H1-hESC	embryonic stem cell:	embryo
50	chr19:42550298-42550348	GM19239	blood:	n/a

(count:9 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 114 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:114 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10407506	chr19:42549934-42549935	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs578029291	chr19:42549941-42549942	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs531381212	chr19:42549950-42549951	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs549934846	chr19:42549964-42549965	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs185327261	chr19:42550026-42550027	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs527714861	chr19:42550041-42550042	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs552273680	chr19:42550096-42550097	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs538644923	chr19:42550115-42550116	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs190814435	chr19:42550138-42550139	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs565532466	chr19:42550156-42550157	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs534558231	chr19:42550212-42550213	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs62119594	chr19:42550299-42550300	Weak transcription Strong transcription Enhancers	CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs574211715	chr19:42550396-42550397	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs78069867	chr19:42550432-42550433	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs556260856	chr19:42550503-42550504	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs531709662	chr19:42550520-42550521	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs73051456	chr19:42550576-42550577	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs531279928	chr19:42550622-42550623	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs182615644	chr19:42550632-42550633	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs146837421	chr19:42550657-42550658	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs188950907	chr19:42550662-42550663	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs561006826	chr19:42550681-42550682	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs531546410	chr19:42550694-42550695	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs569088391	chr19:42550731-42550732	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs192242094	chr19:42550740-42550741	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs564985858	chr19:42550793-42550794	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs532287692	chr19:42550835-42550836	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs183146816	chr19:42550837-42550838	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs565699299	chr19:42550851-42550852	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs536422831	chr19:42550883-42550884	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs529644102	chr19:42551006-42551007	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs369490927	chr19:42551039-42551040	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs371380327	chr19:42551045-42551046	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs113505837	chr19:42551102-42551103	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs567836711	chr19:42551150-42551151	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs187597061	chr19:42551163-42551164	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs556297709	chr19:42551164-42551165	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs571496463	chr19:42551232-42551233	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs538793296	chr19:42551259-42551260	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs530564682	chr19:42551262-42551263	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs11882275	chr19:42551281-42551282	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs553951806	chr19:42551292-42551293	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs572436105	chr19:42551345-42551346	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs117655227	chr19:42551365-42551366	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs554867426	chr19:42551366-42551367	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs576220185	chr19:42551374-42551375	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs543734496	chr19:42551404-42551405	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs192028114	chr19:42551425-42551426	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs532325765	chr19:42551434-42551435	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs541163555	chr19:42551467-42551468	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:61)

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

Chromatin state (count:168 , 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	chr19:42546600-42550200	Weak transcription	Brain Anterior Caudate	brain
27	chr19:42546600-42556800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:42546600-42557600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:42546600-42559000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:42547000-42556800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:42547200-42555800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:42547800-42550400	Strong transcription	Fetal Stomach	stomach
33	chr19:42548600-42550400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:42548600-42551000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr19:42548800-42551600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:42549000-42550000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:42549200-42550200	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr19:42549200-42550400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr19:42549200-42550400	Strong transcription	Aorta	Aorta
40	chr19:42549200-42550600	Strong transcription	Brain Germinal Matrix	brain
41	chr19:42549200-42551000	Strong transcription	Brain Angular Gyrus	brain
42	chr19:42549200-42551200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr19:42549600-42554800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:42549600-42556400	Weak transcription	Fetal Brain Male	brain
45	chr19:42549800-42553600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr19:42549800-42556400	Strong transcription	Fetal Brain Female	brain
47	chr19:42549800-42563200	Weak transcription	Fetal Intestine Small	intestine
48	chr19:42550000-42553600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:42550200-42550600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr19:42550200-42550800	Enhancers	Brain Anterior Caudate	brain

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