Variant report

Variant	nsv828648
Chromosome Location	chr19:56861685-56864862
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	chr19:56861841-56862087	K562	blood:	n/a	n/a
2	ARID3A	chr19:56861841-56862098	HepG2	liver:	n/a	n/a
3	ATF1	chr19:56861870-56862141	K562	blood:	n/a	n/a
4	BHLHE40	chr19:56861839-56862108	GM12878	blood:	n/a	n/a
5	CBX3	chr19:56861759-56862199	K562	blood:	n/a	n/a
6	CEBPB	chr19:56861866-56862166	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr19:56861856-56862111	MCF-7	breast:	n/a	n/a
8	CEBPB	chr19:56861840-56862188	K562	blood:	n/a	n/a
9	CEBPB	chr19:56864074-56864274	HepG2	liver:	n/a	n/a
10	CTCF	chr19:56861900-56862050	Caco-2	colon:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
11	CTCF	chr19:56861917-56862134	MCF-7	breast:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
12	CTCF	chr19:56861843-56862173	HUVEC	blood vessel:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
13	CTCF	chr19:56861920-56862070	A549	lung:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
14	CTCF	chr19:56861980-56862130	GM12871	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
15	CTCF	chr19:56861940-56862090	GM12875	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
16	CTCF	chr19:56861940-56862090	WERI-Rb-1	eye:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
17	CTCF	chr19:56861880-56862030	GM12866	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
18	CTCF	chr19:56861880-56862030	GM12872	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
19	CTCF	chr19:56861960-56862110	AoAF	blood vessel:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
20	CTCF	chr19:56862314-56862406	ProgFib	skin:	n/a	n/a
21	CTCF	chr19:56861960-56862110	GM12874	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
22	CTCF	chr19:56861860-56862010	HMEC	breast:	n/a	n/a
23	CTCF	chr19:56861759-56862200	MCF-7	breast:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
24	CTCF	chr19:56861940-56862090	GM12871	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
25	CTCF	chr19:56861960-56862110	AG09309	skin:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
26	CTCF	chr19:56861900-56862050	GM12864	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
27	CTCF	chr19:56861968-56862112	A549	lung:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
28	CTCF	chr19:56861881-56862157	Pancreas_OC	pancreas:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
29	CTCF	chr19:56861940-56862090	HMF	breast:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
30	CTCF	chr19:56862339-56862376	GM10266	blood:	n/a	n/a
31	CTCF	chr19:56862297-56862396	GM19240	blood:	n/a	n/a
32	CTCF	chr19:56862380-56862530	WI-38	lung:	n/a	n/a
33	CTCF	chr19:56861940-56862090	MCF-7	breast:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
34	CTCF	chr19:56861960-56862110	GM12864	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
35	CTCF	chr19:56861960-56862110	GM12873	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
36	CTCF	chr19:56861797-56862176	HepG2	liver:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
37	CTCF	chr19:56861841-56862167	Spleen_OC	spleen:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
38	CTCF	chr19:56862287-56862399	GM12891	blood:	n/a	n/a
39	CTCF	chr19:56861869-56862156	Medullo	brain:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
40	CTCF	chr19:56862293-56862393	NHEK	skin:	n/a	n/a
41	CTCF	chr19:56861896-56862144	Gliobla	brain:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
42	CTCF	chr19:56861940-56862090	HCFaa	heart:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
43	CTCF	chr19:56861861-56862140	Kidney_OC	kidney:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
44	CTCF	chr19:56861920-56862070	NB4	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
45	CTCF	chr19:56861940-56862090	AG04450	lung:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
46	CTCF	chr19:56862300-56862450	SAEC	small airway:	n/a	n/a
47	CTCF	chr19:56861940-56862090	GM12873	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023
48	CTCF	chr19:56862293-56862368	GM13977	blood:	n/a	n/a
49	CTCF	chr19:56861860-56862010	NHDF-neo	bronchial:	n/a	n/a
50	CTCF	chr19:56861881-56862161	K562	blood:	n/a	chr19:56862006-56862024 chr19:56862001-56862022 chr19:56862007-56862023

No.	Distal block	Cell Line	Cell type
1	chr19:56861231..56864651-chr19:56864910..56868187,3	K562	blood:
2	chr19:56861231..56863974-chr19:56864374..56866865,3	K562	blood:
3	chr19:56668300..56669866-chr19:56860009..56861949,2	K562	blood:
4	chr19:56821112..56821613-chr19:56861782..56862434,2	K562	blood:
5	chr19:56587879..56588429-chr19:56861518..56862050,2	MCF-7	breast:
6	chr19:56825650..56827475-chr19:56859296..56861906,3	K562	blood:
7	chr19:56861231..56863974-chr19:56864374..56866865,3	K562	blood:
8	chr19:56821792..56823459-chr19:56860076..56862047,2	K562	blood:

Variant related genes	Relation type
ENSG00000267429	TF binding region
ENSG00000267549	chromatin interactions
ENSG00000131848	chromatin interactions
ENSG00000167685	chromatin interactions

Extended variants
information (count: 101 )
Associated
traits (count: 68 )

Variant overlapped rSNPs/rCNVs (count:101 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs560472634	chr19:56861694-56861695	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs191934814	chr19:56861707-56861708	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs575497121	chr19:56861726-56861727	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs114517946	chr19:56861846-56861847	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs11671109	chr19:56861932-56861933	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs12982404	chr19:56862069-56862070	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs540711652	chr19:56862163-56862164	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs183032881	chr19:56862196-56862197	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs532655691	chr19:56862197-56862198	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs200356796	chr19:56862218-56862219	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs571701858	chr19:56862226-56862227	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs142779790	chr19:56862228-56862229	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs562906103	chr19:56862285-56862286	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs146073173	chr19:56862320-56862321	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs368741449	chr19:56862362-56862363	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs186701530	chr19:56862366-56862367	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs148476723	chr19:56862367-56862368	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs536021519	chr19:56862377-56862378	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs141813544	chr19:56862395-56862396	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs11667517	chr19:56862467-56862468	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs538359400	chr19:56862587-56862588	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs536827945	chr19:56862718-56862719	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs574919455	chr19:56862753-56862754	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs373427546	chr19:56862869-56862870	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs538525723	chr19:56862904-56862905	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs75106529	chr19:56862909-56862910	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs79972086	chr19:56862910-56862911	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs533765029	chr19:56862944-56862945	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs560688803	chr19:56862953-56862954	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs2058318	chr19:56862976-56862977	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs190378003	chr19:56862997-56862998	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs562868184	chr19:56863001-56863002	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs531651787	chr19:56863027-56863028	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs548576094	chr19:56863066-56863067	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs560980972	chr19:56863077-56863078	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs371933795	chr19:56863107-56863108	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs8109340	chr19:56863145-56863146	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs370231943	chr19:56863167-56863168	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs546351661	chr19:56863187-56863188	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs77819594	chr19:56863192-56863193	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs11672336	chr19:56863207-56863208	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs369252788	chr19:56863209-56863210	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs139573357	chr19:56863222-56863223	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs556126006	chr19:56863249-56863250	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs537402155	chr19:56863285-56863286	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs554552368	chr19:56863291-56863292	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs2058319	chr19:56863306-56863307	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs534532305	chr19:56863307-56863308	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs8109555	chr19:56863358-56863359	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs577561224	chr19:56863372-56863373	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:68)

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
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Colorectal cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Alzheimer''s disease	22166940	CNVD
Heart disease	21282601	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Glioblastoma multiforme	21922591	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56854200-56863200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr19:56855000-56870200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr19:56859400-56872800	Weak transcription	Ovary	ovary
4	chr19:56859600-56862400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:56859600-56862400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:56860000-56862800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:56861600-56862000	Enhancers	Colon Smooth Muscle	Colon
8	chr19:56861800-56862000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:56862000-56868400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:56862400-56863000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:56862400-56863400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr19:56862400-56866400	Weak transcription	Right Atrium	heart
13	chr19:56862800-56863400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr19:56863000-56872800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:56863800-56864000	Enhancers	Brain Substantia Nigra	brain
16	chr19:56863800-56864600	Enhancers	HepG2	liver
17	chr19:56864000-56864400	Enhancers	Brain Hippocampus Middle	brain
18	chr19:56864000-56864400	Weak transcription	Brain Substantia Nigra	brain
19	chr19:56864400-56864600	ZNF genes & repeats	Brain Substantia Nigra	brain
20	chr19:56864400-56864800	ZNF genes & repeats	Liver	Liver
21	chr19:56864600-56865600	Weak transcription	Brain Substantia Nigra	brain
22	chr19:56864600-56865800	Weak transcription	HepG2	liver
23	chr19:56864800-56865400	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links