Variant report

Variant	esv3436794
Chromosome Location	chr19:53422240-53424938
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:8)
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	FOXA2	chr19:53423600-53423896	A549	lung:	n/a	n/a
2	GABPA	chr19:53423714-53423774	HepG2	liver:	n/a	n/a
3	NR2F2	chr19:53423539-53423804	K562	blood:	n/a	n/a
4	PAX5	chr19:53422436-53422659	GM12878	blood:	n/a	n/a
5	PAX5	chr19:53422427-53422738	GM12878	blood:	n/a	n/a
6	PAX5	chr19:53422424-53422626	GM12878	blood:	n/a	n/a
7	PAX5	chr19:53422456-53422686	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:53424300-53424366	K562	blood:	n/a	n/a
9	POLR2A	chr19:53424280-53424751	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:53424670-53424720	ECC-1	luminal epithelium:	n/a
2	chr19:53424670-53424720	NHDF-neo	bronchial:	n/a
3	chr19:53424670-53424720	HCM	heart:	n/a
4	chr19:53424670-53424720	AG09319	gingival:	n/a
5	chr19:53424670-53424720	RPTEC	kidney:	n/a
6	chr19:53424670-53424720	GM12891	blood:	n/a
7	chr19:53424670-53424720	HepG2	liver:	n/a
8	chr19:53424670-53424720	MCF10A-Er-Src	breast:	n/a
9	chr19:53424670-53424720	HEK293	kidney:	embryo
10	chr19:53424670-53424720	HCPEpiC	choroid plexus:	n/a
11	chr19:53424670-53424720	GM12878	blood:	n/a
12	chr19:53424670-53424720	ProgFib	skin:	n/a
13	chr19:53424670-53424720	BJ	skin:	n/a
14	chr19:53424670-53424720	AG04449	skin:	fetal
15	chr19:53424670-53424720	NH-A	brain:	n/a
16	chr19:53424670-53424720	U87	brain:	n/a
17	chr19:53424670-53424720	LNCaP	prostate:	n/a
18	chr19:53424670-53424720	K562	blood:	n/a
19	chr19:53424670-53424720	HUVEC	blood vessel:	n/a
20	chr19:53424670-53424720	MCF-7	breast:	n/a
21	chr19:53424670-53424720	NT2-D1	testis:	n/a
22	chr19:53424670-53424720	A549	lung:	n/a
23	chr19:53424670-53424720	HAEpiC	amniotic membrane:	n/a
24	chr19:53424670-53424720	SAEC	small airway:	n/a
25	chr19:53424670-53424720	PFSK-1	brain:	n/a
26	chr19:53424670-53424720	IMR90	lung:	fetal
27	chr19:53424670-53424720	SKMC	muscle:	n/a
28	chr19:53424670-53424720	HCF	heart:	n/a
29	chr19:53424670-53424720	Hela-S3	cervix:	n/a
30	chr19:53424670-53424720	HCT-116	colon:	n/a
31	chr19:53424670-53424720	AoSMC	blood vessel:	n/a
32	chr19:53424670-53424720	ovcar-3	ovarian:	n/a
33	chr19:53424670-53424720	HL-60	blood:	n/a
34	chr19:53424670-53424720	HRCEpiC	kidney:	n/a
35	chr19:53424670-53424720	GM12892	blood:	n/a
36	chr19:53424670-53424720	NB4	blood:	n/a
37	chr19:53424670-53424720	SK-N-SH_RA	brain:	n/a
38	chr19:53424670-53424720	T-47D	breast:	n/a
39	chr19:53424670-53424720	Caco-2	colon:	n/a
40	chr19:53424670-53424720	SK-N-MC	brain:	n/a
41	chr19:53424670-53424720	AG10803	skin:	n/a
42	chr19:53424670-53424720	HIPEpiC	eye:	n/a
43	chr19:53424670-53424720	GM19239	blood:	n/a
44	chr19:53424670-53424720	AG04450	lung:	fetal
45	chr19:53424670-53424720	H1-hESC	embryonic stem cell:	embryo
46	chr19:53424670-53424720	HMEC	breast:	n/a
47	chr19:53424670-53424720	HRPEpiC	eye:	n/a
48	chr19:53424670-53424720	HRE	kidney:	n/a
49	chr19:53424670-53424720	HNPCEpiC	eye:	n/a
50	chr19:53424670-53424720	Hepatocyte	liver:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:53418400..53422745-chr19:53423096..53427800,7	K562	blood:
2	chr19:53419869..53422803-chr19:53423217..53426977,4	K562	blood:
3	chr19:53419869..53422803-chr19:53423217..53426977,4	K562	blood:
4	chr19:53424791..53427731-chr19:53464365..53467863,4	K562	blood:
5	chr19:53359564..53361265-chr19:53424872..53426783,2	MCF-7	breast:
6	chr19:53399773..53402425-chr19:53424830..53427617,2	MCF-7	breast:
7	chr19:53418400..53422745-chr19:53423096..53427800,7	K562	blood:
8	chr19:53424714..53426568-chr19:53443432..53446550,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269646	TF binding region
ZNF888	TF binding region
ENSG00000269646	CpG island
ZNF888	CpG island
ENSG00000213793	chromatin interactions
ENSG00000269646	chromatin interactions
ENSG00000221874	chromatin interactions
ENSG00000198538	chromatin interactions
ENSG00000213801	chromatin interactions
ENSG00000182986	chromatin interactions
ENSG00000180257	chromatin interactions
ENSG00000204604	chromatin interactions

Extended variants
information (count: 82 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:82 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs186067658	chr19:53422411-53422412	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs62116780	chr19:53422427-53422428	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs113865838	chr19:53422433-53422434	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs566587559	chr19:53422476-53422477	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs534038535	chr19:53422484-53422485	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs377718702	chr19:53422565-53422566	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs576946521	chr19:53422566-53422567	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs369603548	chr19:53422568-53422569	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs544129224	chr19:53422573-53422574	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs28558869	chr19:53422593-53422594	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs556493630	chr19:53422651-53422652	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs574826158	chr19:53422703-53422704	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs28647955	chr19:53422734-53422735	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs370544542	chr19:53422753-53422754	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs560191070	chr19:53422795-53422796	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs183195545	chr19:53422803-53422804	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs75207442	chr19:53422824-53422825	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs540650576	chr19:53422879-53422880	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs564244455	chr19:53422941-53422942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs532578874	chr19:53422945-53422946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs551204834	chr19:53422959-53422960	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs533622323	chr19:53422985-53422986	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs377582629	chr19:53423048-53423049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs569200417	chr19:53423056-53423057	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs200898285	chr19:53423074-53423075	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs530337322	chr19:53423164-53423165	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs113774133	chr19:53423227-53423228	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs550283773	chr19:53423279-53423280	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs368267688	chr19:53423280-53423281	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs192755306	chr19:53423424-53423425	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs182050093	chr19:53423438-53423439	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs374692170	chr19:53423482-53423483	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs558760077	chr19:53423503-53423504	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs533299968	chr19:53423519-53423520	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs28482940	chr19:53423532-53423533	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs556401736	chr19:53423533-53423534	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs112613189	chr19:53423561-53423562	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs373109136	chr19:53423593-53423594	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs542164932	chr19:53423610-53423611	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs553764736	chr19:53423642-53423643	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs28594228	chr19:53423651-53423652	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs571928177	chr19:53423652-53423653	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs28557324	chr19:53423658-53423659	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs28587663	chr19:53423660-53423661	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs545814420	chr19:53423667-53423668	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs28564324	chr19:53423764-53423765	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs200397466	chr19:53423770-53423771	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs201549254	chr19:53423780-53423781	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs78300892	chr19:53423785-53423786	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs77525816	chr19:53423802-53423803	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:67)

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
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	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
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian cancer	22174824	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Wilms tumour	21544195	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	18852474	CNVD
Glioblastoma multiforme	17002787	CNVD
Cervical cancer	21062161	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	16573809	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Melanoma	17363583	CNVD
Breast cancer	21785460	CNVD
Adrenocortical carcinoma	18281524	CNVD
Melanoma	20877625	CNVD
Lung adenocarcinoma	21935476	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:140 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53401000-53425600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:53401400-53425600	Weak transcription	NHDF-Ad	bronchial
3	chr19:53401400-53425800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:53401600-53425600	Weak transcription	Brain Hippocampus Middle	brain
5	chr19:53401600-53425600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr19:53401600-53426000	Weak transcription	Brain Substantia Nigra	brain
7	chr19:53401800-53425600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr19:53401800-53426000	Weak transcription	Brain Angular Gyrus	brain
9	chr19:53401800-53426000	Weak transcription	Right Ventricle	heart
10	chr19:53402000-53425800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:53402000-53425800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr19:53409600-53425600	Weak transcription	Fetal Kidney	kidney
13	chr19:53410400-53425400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:53410800-53425000	Weak transcription	Stomach Mucosa	stomach
15	chr19:53410800-53425000	Weak transcription	HepG2	liver
16	chr19:53410800-53425800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:53411400-53425600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:53411400-53425600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr19:53411400-53425600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:53411400-53425600	Weak transcription	HUVEC	blood vessel
21	chr19:53411400-53425800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:53411400-53425800	Weak transcription	Brain Anterior Caudate	brain
23	chr19:53411400-53426000	Weak transcription	HSMM	muscle
24	chr19:53411600-53425600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr19:53411600-53425800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:53411800-53425600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:53411800-53425600	Weak transcription	HMEC	breast
28	chr19:53412000-53426000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr19:53412200-53425800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:53412400-53425600	Weak transcription	Colonic Mucosa	Colon
31	chr19:53413600-53425800	Weak transcription	Colon Smooth Muscle	Colon
32	chr19:53414600-53425600	Weak transcription	Small Intestine	intestine
33	chr19:53416000-53426000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr19:53416400-53425600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:53416800-53425600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr19:53417600-53425600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:53417600-53425600	Weak transcription	Osteobl	bone
38	chr19:53417600-53425800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr19:53417800-53425000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:53418000-53425800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:53418200-53425000	Weak transcription	Fetal Thymus	thymus
42	chr19:53418200-53425600	Weak transcription	Adipose Nuclei	Adipose
43	chr19:53418200-53425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr19:53418200-53425800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr19:53418400-53425000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:53418400-53425600	Weak transcription	Primary B cells from cord blood	blood
47	chr19:53419400-53424600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:53419400-53426200	Weak transcription	Aorta	Aorta
49	chr19:53419600-53425600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr19:53419600-53425600	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links