Variant report

Variant	nsv1062518
Chromosome Location	chr19:38540454-38564913
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:302)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:302 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr19:38548703-38548978	HepG2	liver:	n/a	n/a
2	BACH1	chr19:38561235-38561692	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr19:38561245-38561575	K562	blood:	n/a	n/a
4	BHLHE40	chr19:38553628-38553846	K562	blood:	n/a	n/a
5	BHLHE40	chr19:38538477-38540624	GM12878	blood:	n/a	chr19:38539133-38539142 chr19:38539132-38539141 chr19:38539127-38539148 chr19:38539131-38539144 chr19:38539133-38539142 chr19:38539134-38539143
6	BHLHE40	chr19:38550520-38551258	GM12878	blood:	n/a	n/a
7	BHLHE40	chr19:38550580-38550894	K562	blood:	n/a	n/a
8	CEBPB	chr19:38545880-38545921	H1-hESC	embryonic stem cell:	n/a	n/a
9	CEBPB	chr19:38550091-38550415	IMR90	lung:	n/a	chr19:38550263-38550274
10	CEBPB	chr19:38563725-38564073	IMR90	lung:	n/a	n/a
11	CEBPB	chr19:38548728-38548865	HepG2	liver:	n/a	n/a
12	CEBPB	chr19:38564855-38565218	HepG2	liver:	n/a	n/a
13	CEBPB	chr19:38563898-38563917	HepG2	liver:	n/a	n/a
14	CEBPB	chr19:38550183-38550396	HepG2	liver:	n/a	chr19:38550263-38550274
15	CEBPB	chr19:38548703-38549012	HepG2	liver:	n/a	n/a
16	CREB1	chr19:38552047-38552372	A549	lung:	n/a	n/a
17	CREB1	chr19:38548608-38549143	A549	lung:	n/a	n/a
18	CTCF	chr19:38554080-38554230	HCPEpiC	choroid plexus:	n/a	n/a
19	CTCF	chr19:38564900-38565050	HBMEC	blood vessel:	n/a	n/a
20	CTCF	chr19:38546400-38546550	HBMEC	blood vessel:	n/a	n/a
21	CTCF	chr19:38546340-38546490	HRE	kidney:	n/a	n/a
22	CTCF	chr19:38555206-38555232	Kidney_OC	kidney:	n/a	n/a
23	CTCF	chr19:38554000-38554150	SK-N-SH_RA	brain:	n/a	n/a
24	CTCF	chr19:38546380-38546530	HA-sp	spinal cord:	n/a	n/a
25	CTCF	chr19:38546360-38546510	AG09319	gingival:	n/a	n/a
26	CTCF	chr19:38546355-38546575	IMR90	lung:	n/a	n/a
27	CTCF	chr19:38546300-38546450	WERI-Rb-1	eye:	n/a	n/a
28	CTCF	chr19:38546400-38546550	HPAF	blood vessel:	n/a	n/a
29	CTCF	chr19:38546400-38546550	NHDF-neo	bronchial:	n/a	n/a
30	CTCF	chr19:38546320-38546470	HPF	lung:	n/a	n/a
31	CTCF	chr19:38546360-38546510	A549	lung:	n/a	n/a
32	CTCF	chr19:38546300-38546450	HPF	lung:	n/a	n/a
33	CTCF	chr19:38546400-38546550	AG04450	lung:	n/a	n/a
34	CTCF	chr19:38546420-38546570	MCF-7	breast:	n/a	n/a
35	CTCF	chr19:38546415-38546495	MCF-7	breast:	n/a	n/a
36	CTCF	chr19:38549000-38549150	Caco-2	colon:	n/a	n/a
37	CTCF	chr19:38546240-38546390	GM12868	blood:	n/a	n/a
38	CTCF	chr19:38546320-38546470	HCM	heart:	n/a	n/a
39	CTCF	chr19:38554020-38554170	SK-N-SH_RA	brain:	n/a	n/a
40	CTCF	chr19:38546360-38546510	HPAF	blood vessel:	n/a	n/a
41	CTCF	chr19:38546320-38546470	HEK293	kidney:	n/a	n/a
42	CTCF	chr19:38546500-38546650	HMF	breast:	n/a	n/a
43	CTCF	chr19:38546340-38546490	HBMEC	blood vessel:	n/a	n/a
44	CTCF	chr19:38546450-38546465	Kidney_OC	kidney:	n/a	n/a
45	CTCF	chr19:38546380-38546530	HCPEpiC	choroid plexus:	n/a	n/a
46	CTCF	chr19:38546400-38546550	AG10803	skin:	n/a	n/a
47	CTCF	chr19:38546360-38546510	HCPEpiC	choroid plexus:	n/a	n/a
48	CTCF	chr19:38546300-38546450	HRPEpiC	eye:	n/a	n/a
49	CTCF	chr19:38546393-38546496	HUVEC	blood vessel:	n/a	n/a
50	CTCF	chr19:38546400-38546550	SAEC	small airway:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:38546251..38550140-chr19:38563809..38566619,4	MCF-7	breast:
2	chr19:38549096..38551828-chr19:38559673..38561442,2	MCF-7	breast:
3	chr19:38547326..38550182-chr19:38558061..38560076,2	MCF-7	breast:
4	chr19:38395738..38398220-chr19:38547451..38552123,4	MCF-7	breast:
5	chr19:38537912..38540463-chr19:38546396..38548192,2	MCF-7	breast:
6	chr19:38547570..38550382-chr19:38704917..38707515,2	MCF-7	breast:
7	chr19:38543891..38548790-chr19:38549215..38554298,5	MCF-7	breast:
8	chr19:38395958..38396771-chr19:38564609..38565146,2	MCF-7	breast:
9	chr19:38546251..38550140-chr19:38563809..38566619,4	MCF-7	breast:
10	chr19:38536919..38539857-chr19:38546336..38549033,2	MCF-7	breast:
11	chr19:38540614..38543298-chr19:38547451..38549328,2	MCF-7	breast:
12	chr19:38550744..38552362-chr19:38559660..38561600,2	MCF-7	breast:
13	chr19:38537912..38540463-chr19:38546396..38548192,2	MCF-7	breast:
14	chr19:38396259..38398778-chr19:38548005..38550219,2	MCF-7	breast:
15	chr19:38540614..38543298-chr19:38547451..38549328,2	MCF-7	breast:
16	chr19:38395351..38397718-chr19:38560093..38561831,2	MCF-7	breast:
17	chr19:38393370..38393940-chr19:38564690..38565216,2	MCF-7	breast:
18	chr19:38535066..38537554-chr19:38539866..38542740,2	MCF-7	breast:
19	chr19:38481055..38481656-chr19:38564723..38565599,2	MCF-7	breast:
20	chr19:38549096..38551828-chr19:38559673..38561442,2	MCF-7	breast:
21	chr19:38440998..38442982-chr19:38537686..38540589,2	MCF-7	breast:
22	chr19:38550744..38552362-chr19:38559660..38561600,2	MCF-7	breast:
23	chr19:38547326..38550182-chr19:38558061..38560076,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPINT2-8	chr19:38556989-38557339	expReg_chr19_4921_+

No data

Variant related genes	Relation type
ENSG00000221258	TF binding region
ENSG00000171804	chromatin interactions
ENSG00000105738	chromatin interactions
ENSG00000011332	chromatin interactions
ENSG00000221258	chromatin interactions

Extended variants
information (count: 950 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:950 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs142282547	chr19:38540455-38540456	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
2	rs545375102	chr19:38540473-38540474	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
3	rs376691198	chr19:38540493-38540494	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
4	rs1654341	chr19:38540746-38540747	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs527680978	chr19:38540817-38540818	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs567439384	chr19:38540820-38540821	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs556865814	chr19:38540858-38540859	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs529059524	chr19:38540886-38540887	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs550533024	chr19:38540924-38540925	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs569119807	chr19:38540955-38540956	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs539392687	chr19:38540957-38540958	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs557783700	chr19:38540969-38540970	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs566430212	chr19:38540970-38540971	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs533780418	chr19:38540978-38540979	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs189183475	chr19:38540990-38540991	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs67888223	chr19:38541032-38541033	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs573806669	chr19:38541037-38541038	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs544775708	chr19:38541111-38541112	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs1612361	chr19:38541114-38541115	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs150832931	chr19:38541123-38541124	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs545327833	chr19:38541126-38541127	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs139246653	chr19:38541134-38541135	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs527642827	chr19:38541173-38541174	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs191685944	chr19:38541190-38541191	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs561026031	chr19:38541206-38541207	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs1725462	chr19:38541207-38541208	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
27	rs150020955	chr19:38541234-38541235	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs569003805	chr19:38541250-38541251	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs566470330	chr19:38541256-38541257	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs533155679	chr19:38541269-38541270	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs62121394	chr19:38541284-38541285	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs147693249	chr19:38541289-38541290	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs539239472	chr19:38541311-38541312	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs184236744	chr19:38541358-38541359	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs116706106	chr19:38541380-38541381	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs568027585	chr19:38541381-38541382	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs537589473	chr19:38541417-38541418	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs556224460	chr19:38541434-38541435	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs578078929	chr19:38541542-38541543	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs1616705	chr19:38541593-38541594	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs1725463	chr19:38541690-38541691	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs144368043	chr19:38541728-38541729	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs111784791	chr19:38541738-38541739	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs539596491	chr19:38541742-38541743	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs553411097	chr19:38541764-38541765	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs560990942	chr19:38541790-38541791	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs576479026	chr19:38541799-38541800	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs543504893	chr19:38541800-38541801	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs377376949	chr19:38541859-38541860	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs148895690	chr19:38541879-38541880	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:62)

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
Pleomorphic liposarcoma	18784837	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
Disorders of sex development	21048976	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
Lung cancer	18438408	CNVD
Wilms tumour	21544195	CNVD
Mental retardation	19951919	CNVD
19q13.11 deletion syndrome	22378287	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Lung cancer	21569311	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	21509527	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Gastric cancer	17229543	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:770 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38521800-38548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:38526800-38545600	Weak transcription	Stomach Mucosa	stomach
4	chr19:38527800-38548800	Weak transcription	Right Atrium	heart
5	chr19:38527800-38551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
7	chr19:38528800-38543400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr19:38529000-38548600	Weak transcription	Pancreas	Pancrea
9	chr19:38531400-38550800	Weak transcription	NHLF	lung
10	chr19:38534200-38540600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:38534200-38540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:38534400-38543200	Strong transcription	Fetal Intestine Small	intestine
13	chr19:38534800-38545400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:38536000-38540800	Enhancers	Primary hematopoietic stem cells	blood
15	chr19:38536200-38540800	Enhancers	Fetal Thymus	thymus
16	chr19:38536200-38543400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:38537800-38545400	Weak transcription	Fetal Stomach	stomach
18	chr19:38537800-38548800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:38537800-38548800	Weak transcription	Esophagus	oesophagus
20	chr19:38538000-38548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:38538400-38543400	Weak transcription	Fetal Intestine Large	intestine
22	chr19:38538400-38552800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:38538600-38543200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:38538800-38540600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr19:38538800-38540600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr19:38539000-38545200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:38539000-38545400	Weak transcription	Gastric	stomach
28	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
29	chr19:38539200-38543000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:38539200-38545200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:38539200-38545200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:38539200-38545400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:38539200-38545400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:38539200-38548800	Weak transcription	Colonic Mucosa	Colon
35	chr19:38539200-38548800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
37	chr19:38539400-38540800	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr19:38539600-38545400	Weak transcription	HSMM	muscle
39	chr19:38540000-38540600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:38540000-38540600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:38540000-38540600	Enhancers	Lung	lung
42	chr19:38540000-38540600	Enhancers	Spleen	Spleen
43	chr19:38540000-38540800	Flanking Active TSS	GM12878-XiMat	blood
44	chr19:38540200-38540600	Enhancers	H1 Cell Line	embryonic stem cell
45	chr19:38540200-38540600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr19:38540200-38540600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr19:38540200-38540600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:38540200-38540600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:38540200-38540600	Enhancers	Thymus	Thymus
50	chr19:38540200-38540800	Enhancers	Primary T cells fromperipheralblood	blood

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