Variant report

Variant	nsv817835
Chromosome Location	chr19:40132825-40162019
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	CEBPB	chr19:40136019-40136106	HepG2	liver:	n/a	chr19:40136071-40136082 chr19:40136071-40136082 chr19:40136072-40136083
2	CEBPB	chr19:40140585-40140785	HepG2	liver:	n/a	chr19:40140634-40140645
3	CEBPB	chr19:40151350-40151658	Hela-S3	cervix:	n/a	chr19:40151501-40151514
4	CTCF	chr19:40148780-40148930	GM12874	blood:	n/a	n/a
5	CTCF	chr19:40156413-40156447	GM20000	blood:	n/a	n/a
6	CTCF	chr19:40136165-40136226	Fibrobl	skin:	n/a	n/a
7	E2F6	chr19:40161693-40162007	H1-hESC	embryonic stem cell:	n/a	n/a
8	EBF1	chr19:40133101-40133106	GM12878	blood:	n/a	n/a
9	EBF1	chr19:40132538-40132832	GM12878	blood:	n/a	chr19:40132695-40132706
10	EP300	chr19:40132317-40132827	HepG2	liver:	n/a	chr19:40132548-40132558
11	FOS	chr19:40151334-40151672	MCF10A-Er-Src	breast:	n/a	chr19:40151517-40151526 chr19:40151516-40151528 chr19:40151518-40151525
12	FOS	chr19:40151333-40151675	MCF10A-Er-Src	breast:	n/a	chr19:40151517-40151526 chr19:40151516-40151528 chr19:40151518-40151525
13	FOS	chr19:40133214-40133339	MCF10A-Er-Src	breast:	n/a	chr19:40133269-40133281 chr19:40133270-40133280 chr19:40133271-40133278 chr19:40133270-40133279 chr19:40133271-40133280 chr19:40133270-40133280
14	FOS	chr19:40151343-40151668	MCF10A-Er-Src	breast:	n/a	chr19:40151517-40151526 chr19:40151516-40151528 chr19:40151518-40151525
15	FOS	chr19:40151333-40151682	MCF10A-Er-Src	breast:	n/a	chr19:40151517-40151526 chr19:40151516-40151528 chr19:40151518-40151525
16	FOXA1	chr19:40140516-40140710	HepG2	liver:	n/a	n/a
17	FOXA2	chr19:40140496-40140782	HepG2	liver:	n/a	n/a
18	JUND	chr19:40151403-40151599	HepG2	liver:	n/a	chr19:40151517-40151526 chr19:40151516-40151527 chr19:40151516-40151528 chr19:40151518-40151525
19	MAX	chr19:40161695-40162051	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr19:40161710-40161984	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr19:40161699-40161990	H1-hESC	embryonic stem cell:	n/a	n/a
22	MYC	chr19:40161304-40161411	MCF10A-Er-Src	breast:	n/a	n/a
23	MYC	chr19:40147948-40148032	HUVEC	blood vessel:	n/a	n/a
24	MYC	chr19:40147057-40147151	H1-hESC	embryonic stem cell:	n/a	n/a
25	NFYA	chr19:40136295-40136493	GM12878	blood:	n/a	n/a
26	PAX5	chr19:40150507-40150766	GM12878	blood:	n/a	chr19:40150609-40150618 chr19:40150652-40150661
27	PAX5	chr19:40150530-40150770	GM12878	blood:	n/a	chr19:40150609-40150618 chr19:40150652-40150661
28	POLR2A	chr19:40139537-40140267	K562	blood:	n/a	n/a
29	POLR2A	chr19:40138588-40138769	K562	blood:	n/a	n/a
30	POLR2A	chr19:40141089-40141348	K562	blood:	n/a	n/a
31	POLR2A	chr19:40147042-40147108	MCF-7	breast:	n/a	n/a
32	POU2F2	chr19:40161680-40162006	GM12891	blood:	n/a	n/a
33	RCOR1	chr19:40136617-40136682	GM12878	blood:	n/a	n/a
34	RCOR1	chr19:40151356-40151553	Hela-S3	cervix:	n/a	n/a
35	RCOR1	chr19:40136485-40136878	IMR90	lung:	n/a	n/a
36	REST	chr19:40135905-40137053	A549	lung:	n/a	chr19:40136647-40136667 chr19:40136647-40136656 chr19:40136652-40136661 chr19:40136648-40136666 chr19:40136655-40136665 chr19:40136650-40136663 chr19:40136647-40136667 chr19:40136653-40136667 chr19:40136647-40136667 chr19:40136647-40136660 chr19:40136650-40136663
37	REST	chr19:40136454-40136805	K562	blood:	n/a	chr19:40136647-40136667 chr19:40136647-40136656 chr19:40136652-40136661 chr19:40136648-40136666 chr19:40136655-40136665 chr19:40136650-40136663 chr19:40136647-40136667 chr19:40136653-40136667 chr19:40136647-40136667 chr19:40136647-40136660 chr19:40136650-40136663
38	REST	chr19:40136275-40136835	PFSK-1	brain:	n/a	chr19:40136647-40136667 chr19:40136647-40136656 chr19:40136652-40136661 chr19:40136648-40136666 chr19:40136655-40136665 chr19:40136650-40136663 chr19:40136647-40136667 chr19:40136653-40136667 chr19:40136647-40136667 chr19:40136647-40136660 chr19:40136650-40136663
39	REST	chr19:40138578-40138882	MCF-7	breast:	n/a	n/a
40	REST	chr19:40136758-40136847	GM12878	blood:	n/a	n/a
41	REST	chr19:40136220-40136927	U87	brain:	n/a	chr19:40136647-40136667 chr19:40136647-40136656 chr19:40136652-40136661 chr19:40136648-40136666 chr19:40136655-40136665 chr19:40136650-40136663 chr19:40136647-40136667 chr19:40136653-40136667 chr19:40136647-40136667 chr19:40136647-40136660 chr19:40136650-40136663
42	REST	chr19:40136155-40137069	GM12878	blood:	n/a	chr19:40136647-40136667 chr19:40136647-40136656 chr19:40136652-40136661 chr19:40136648-40136666 chr19:40136655-40136665 chr19:40136650-40136663 chr19:40136647-40136667 chr19:40136653-40136667 chr19:40136647-40136667 chr19:40136647-40136660 chr19:40136650-40136663
43	REST	chr19:40138665-40138841	PANC-1	pancreas:	n/a	n/a
44	REST	chr19:40138618-40138926	PFSK-1	brain:	n/a	n/a
45	REST	chr19:40138496-40139090	PANC-1	pancreas:	n/a	n/a
46	REST	chr19:40138673-40138952	HL-60	blood:	n/a	n/a
47	REST	chr19:40136480-40136776	SK-N-SH	brain:	n/a	chr19:40136647-40136667 chr19:40136647-40136656 chr19:40136652-40136661 chr19:40136648-40136666 chr19:40136655-40136665 chr19:40136650-40136663 chr19:40136647-40136667 chr19:40136653-40136667 chr19:40136647-40136667 chr19:40136647-40136660 chr19:40136650-40136663
48	REST	chr19:40136114-40137074	Hela-S3	cervix:	n/a	chr19:40136647-40136667 chr19:40136647-40136656 chr19:40136652-40136661 chr19:40136648-40136666 chr19:40136655-40136665 chr19:40136650-40136663 chr19:40136647-40136667 chr19:40136653-40136667 chr19:40136647-40136667 chr19:40136647-40136660 chr19:40136650-40136663
49	REST	chr19:40135882-40137042	PFSK-1	brain:	n/a	chr19:40136647-40136667 chr19:40136647-40136656 chr19:40136652-40136661 chr19:40136648-40136666 chr19:40136655-40136665 chr19:40136650-40136663 chr19:40136647-40136667 chr19:40136653-40136667 chr19:40136647-40136667 chr19:40136647-40136660 chr19:40136650-40136663
50	REST	chr19:40136256-40137027	MCF-7	breast:	n/a	chr19:40136647-40136667 chr19:40136647-40136656 chr19:40136652-40136661 chr19:40136648-40136666 chr19:40136655-40136665 chr19:40136650-40136663 chr19:40136647-40136667 chr19:40136653-40136667 chr19:40136647-40136667 chr19:40136647-40136660 chr19:40136650-40136663

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40055301..40057183-chr19:40147250..40149926,2	MCF-7	breast:
2	chr19:39925057..39927468-chr19:40150682..40153479,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LGALS16-1	chr19:40132792-40133041	NONHSAT066318

Variant related genes	Relation type
LGALS16	TF binding region
ENSG00000268243	TF binding region
ENSG00000196235	chromatin interactions
ENSG00000105193	chromatin interactions

Extended variants
information (count: 914 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:914 , 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	rs2270028	chr19:40132825-40132826	Enhancers Bivalent Enhancer	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs370540139	chr19:40132842-40132843	Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
3	rs537944477	chr19:40132843-40132844	Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
4	rs114193401	chr19:40132900-40132901	Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
5	rs533816611	chr19:40132918-40132919	Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
6	rs190282989	chr19:40132923-40132924	Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
7	rs545710048	chr19:40132941-40132942	Enhancers Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
8	rs2270029	chr19:40133000-40133001	Enhancers Bivalent Enhancer	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs138295341	chr19:40133002-40133003	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs375980020	chr19:40133009-40133010	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs7249348	chr19:40133069-40133070	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs537386743	chr19:40133100-40133101	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs549894107	chr19:40133101-40133102	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs1156815	chr19:40133192-40133193	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs532186467	chr19:40133196-40133197	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs181253429	chr19:40133229-40133230	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs565794200	chr19:40133323-40133324	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs534200362	chr19:40133326-40133327	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs78167081	chr19:40133327-40133328	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs567310296	chr19:40133386-40133387	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs143304935	chr19:40133422-40133423	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs556215579	chr19:40133423-40133424	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs578138065	chr19:40133426-40133427	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs111752670	chr19:40133433-40133434	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs1156816	chr19:40133438-40133439	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs572606170	chr19:40133447-40133448	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs185081875	chr19:40133472-40133473	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs188203530	chr19:40133490-40133491	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs16973555	chr19:40133530-40133531	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs60763119	chr19:40133563-40133564	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs543570666	chr19:40133569-40133570	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs374755040	chr19:40133579-40133580	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs564801120	chr19:40133582-40133583	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs180996204	chr19:40133621-40133622	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs141972757	chr19:40133634-40133635	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs559494107	chr19:40133666-40133667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs529975636	chr19:40133678-40133679	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs142879556	chr19:40133681-40133682	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs535076505	chr19:40133690-40133691	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs146264285	chr19:40133691-40133692	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs60962641	chr19:40133698-40133699	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs141713665	chr19:40133732-40133733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs185381635	chr19:40133737-40133738	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs371453651	chr19:40133756-40133757	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs554119989	chr19:40133781-40133782	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs373654637	chr19:40133796-40133797	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs566255562	chr19:40133835-40133836	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs572178585	chr19:40133935-40133936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs7253489	chr19:40133955-40133956	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs6508893	chr19:40133958-40133959	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:65)

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
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
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
Breast cancer	22522925	CNVD

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40131800-40133600	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr19:40132000-40133400	Enhancers	HepG2	liver
3	chr19:40132200-40133000	Bivalent Enhancer	A549	lung
4	chr19:40132600-40133200	Enhancers	Placenta	Placenta
5	chr19:40133200-40151200	Weak transcription	Placenta	Placenta
6	chr19:40146800-40147000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:40147000-40147200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:40148600-40149400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:40150600-40151200	Bivalent Enhancer	GM12878-XiMat	blood
10	chr19:40152200-40153000	Enhancers	Primary T cells from cord blood	blood
11	chr19:40161200-40162600	Enhancers	H9 Cell Line	embryonic stem cell
12	chr19:40161200-40162600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr19:40161200-40162600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr19:40161200-40162600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:40161200-40162800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr19:40161200-40162800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr19:40161200-40162800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr19:40161200-40162800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr19:40161400-40162600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr19:40161400-40162800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr19:40161800-40162000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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