Variant report

Variant	esv3403741
Chromosome Location	chr19:38600512-38604910
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	BCL3	chr19:38602389-38602782	GM12878	blood:	n/a	n/a
2	BCL3	chr19:38602486-38602862	GM12878	blood:	n/a	n/a
3	CEBPB	chr19:38603856-38604072	A549	lung:	n/a	chr19:38603929-38603942
4	CTCF	chr19:38602681-38602810	MCF-7	breast:	n/a	n/a
5	CTCF	chr19:38602480-38602630	GM12873	blood:	n/a	n/a
6	CTCF	chr19:38603753-38604076	GM12878	blood:	n/a	chr19:38603888-38603909
7	CTCF	chr19:38602220-38602370	GM12873	blood:	n/a	n/a
8	CTCF	chr19:38603887-38603977	GM19240	blood:	n/a	chr19:38603888-38603909
9	CTCF	chr19:38602557-38602733	MCF-7	breast:	n/a	n/a
10	CTCF	chr19:38602650-38602785	GM12891	blood:	n/a	n/a
11	CTCF	chr19:38602592-38602620	MCF-7	breast:	n/a	n/a
12	CTCF	chr19:38603780-38603930	SAEC	small airway:	n/a	chr19:38603888-38603909
13	CTCF	chr19:38603820-38603970	A549	lung:	n/a	chr19:38603888-38603909
14	CTCF	chr19:38602492-38602913	GM19239	blood:	n/a	n/a
15	CTCF	chr19:38603920-38603948	GM19238	blood:	n/a	n/a
16	MAX	chr19:38602512-38602993	NB4	blood:	n/a	chr19:38602899-38602909 chr19:38602848-38602858
17	MAX	chr19:38602384-38602991	HUVEC	blood vessel:	n/a	chr19:38602899-38602909 chr19:38602848-38602858
18	MYC	chr19:38602479-38602810	MCF-7	breast:	n/a	n/a
19	MYC	chr19:38602824-38602830	MCF-7	breast:	n/a	n/a
20	MYC	chr19:38602566-38602618	HUVEC	blood vessel:	n/a	n/a
21	MYC	chr19:38602491-38602800	MCF-7	breast:	n/a	n/a
22	MYC	chr19:38602542-38602905	MCF-7	breast:	n/a	chr19:38602848-38602858
23	MYC	chr19:38602639-38602661	HUVEC	blood vessel:	n/a	n/a
24	MYC	chr19:38602475-38602476	MCF-7	breast:	n/a	n/a
25	MYC	chr19:38602801-38602817	MCF-7	breast:	n/a	n/a
26	MYC	chr19:38602483-38602839	MCF-7	breast:	n/a	n/a
27	MYC	chr19:38602415-38602623	H1-hESC	embryonic stem cell:	n/a	n/a
28	NR2C2	chr19:38602496-38603008	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:38600178-38600602	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:38602391-38602395	MCF-7	breast:	n/a	n/a
31	POLR2A	chr19:38602447-38602910	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:38602255-38603067	GM12892	blood:	n/a	n/a
33	POLR2A	chr19:38602293-38602948	A549	lung:	n/a	n/a
34	POLR2A	chr19:38602434-38602970	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:38602277-38602943	MCF-7	breast:	n/a	n/a
36	POLR2A	chr19:38600989-38601039	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:38602392-38602941	A549	lung:	n/a	n/a
38	POLR2A	chr19:38602453-38602948	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr19:38602044-38603123	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:38602194-38602934	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:38602515-38602784	Gliobla	brain:	n/a	n/a
42	POLR2A	chr19:38602545-38602823	A549	lung:	n/a	n/a
43	POLR2A	chr19:38602595-38602783	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:38602834-38602851	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:38602165-38602373	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:38602436-38602988	A549	lung:	n/a	n/a
47	POLR2A	chr19:38602463-38602874	HepG2	liver:	n/a	n/a
48	POLR2A	chr19:38604368-38604480	A549	lung:	n/a	n/a
49	POLR2A	chr19:38602397-38602827	MCF-7	breast:	n/a	n/a
50	POLR2A	chr19:38602884-38602906	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38604586..38606112-chr19:38715121..38717021,2	K562	blood:
2	chr19:38396450..38399349-chr19:38602232..38604723,2	K562	blood:

Variant related genes	Relation type
ENSG00000268764	TF binding region
SIPA1L3	TF binding region
ENSG00000171804	chromatin interactions
ENSG00000105738	chromatin interactions

Extended variants
information (count: 193 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:193 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs370554943	chr19:38600532-38600533	Weak transcription Strong transcription ZNF genes & repeats	TF binding region	2 gene(s)	Overlapped CNVs	n/a
2	rs566544592	chr19:38600549-38600550	Weak transcription Strong transcription ZNF genes & repeats	TF binding region	2 gene(s)	Overlapped CNVs	n/a
3	rs559903125	chr19:38600649-38600650	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs190952656	chr19:38600650-38600651	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs542257710	chr19:38600757-38600758	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs561081521	chr19:38600815-38600816	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs373894415	chr19:38600816-38600817	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs377112393	chr19:38600819-38600820	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs367639220	chr19:38600823-38600824	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs199856683	chr19:38600824-38600825	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs150394676	chr19:38600858-38600859	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs539232870	chr19:38600900-38600901	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs111269818	chr19:38600904-38600905	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs149241842	chr19:38600905-38600906	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs200828228	chr19:38600929-38600930	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs138105681	chr19:38600934-38600935	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs369986084	chr19:38600972-38600973	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs373447922	chr19:38600981-38600982	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs567247816	chr19:38600982-38600983	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs200090564	chr19:38600988-38600989	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs201959023	chr19:38601013-38601014	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs376861619	chr19:38601017-38601018	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs368988982	chr19:38601028-38601029	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs201043296	chr19:38601035-38601036	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs375908407	chr19:38601041-38601042	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs200433036	chr19:38601042-38601043	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs373032582	chr19:38601055-38601056	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs569841938	chr19:38601105-38601106	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs145171803	chr19:38601119-38601120	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs555956720	chr19:38601121-38601122	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs112226853	chr19:38601143-38601144	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs577378352	chr19:38601145-38601146	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs538560544	chr19:38601283-38601284	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs554082505	chr19:38601287-38601288	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs543804375	chr19:38601313-38601314	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs183477804	chr19:38601371-38601372	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs187378558	chr19:38601444-38601445	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs576218749	chr19:38601448-38601449	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs543501031	chr19:38601470-38601471	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs73930357	chr19:38601502-38601503	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs34181002	chr19:38601592-38601593	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs191866976	chr19:38601625-38601626	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs183618823	chr19:38601640-38601641	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs202045900	chr19:38601661-38601662	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs528494849	chr19:38601665-38601666	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs113372421	chr19:38601669-38601670	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs12976860	chr19:38601670-38601671	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs62121432	chr19:38601684-38601685	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs528910730	chr19:38601698-38601699	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs10404957	chr19:38601728-38601729	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:60)

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
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:258 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:38567600-38605400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:38573600-38610000	Strong transcription	Fetal Intestine Large	intestine
4	chr19:38581600-38610000	Weak transcription	Psoas Muscle	Psoas
5	chr19:38584800-38602400	Weak transcription	Fetal Brain Male	brain
6	chr19:38584800-38602400	Weak transcription	Fetal Heart	heart
7	chr19:38587000-38605400	Strong transcription	Primary B cells from peripheral blood	blood
8	chr19:38587200-38603200	Strong transcription	Primary B cells from cord blood	blood
9	chr19:38587200-38613600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:38587400-38613400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr19:38588600-38604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:38588800-38606600	Strong transcription	Liver	Liver
13	chr19:38589200-38606800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr19:38590200-38605200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:38590200-38605800	Strong transcription	Adipose Nuclei	Adipose
16	chr19:38590200-38606600	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:38590200-38606600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr19:38590200-38611000	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr19:38590400-38606400	Strong transcription	Fetal Brain Female	brain
20	chr19:38590400-38609800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr19:38590800-38602800	Strong transcription	Spleen	Spleen
22	chr19:38590800-38603600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr19:38590800-38603800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr19:38590800-38606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:38590800-38608800	Strong transcription	Fetal Intestine Small	intestine
26	chr19:38591000-38601800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:38591000-38605000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:38591200-38605400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr19:38591200-38605400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:38591200-38605800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr19:38591400-38600800	Weak transcription	Colon Smooth Muscle	Colon
32	chr19:38591400-38603600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr19:38591400-38605400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:38591600-38602600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:38591800-38609000	Strong transcription	Fetal Stomach	stomach
36	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
37	chr19:38592600-38602000	Weak transcription	Fetal Kidney	kidney
38	chr19:38594000-38602000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:38594400-38606800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr19:38594600-38602400	Strong transcription	Lung	lung
41	chr19:38594600-38606800	Strong transcription	GM12878-XiMat	blood
42	chr19:38594800-38603000	Strong transcription	Primary T cells from cord blood	blood
43	chr19:38595400-38603600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:38595800-38603000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:38595800-38605000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr19:38595800-38605800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:38595800-38606200	Strong transcription	Ovary	ovary
48	chr19:38595800-38606600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:38596000-38602400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr19:38596000-38603000	Strong transcription	Brain Anterior Caudate	brain

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