Variant report

Variant	esv3351362
Chromosome Location	chr19:42307636-42311347
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	CTCF	chr19:42309897-42309970	MCF-7	breast:	n/a	chr19:42309918-42309931
2	CTCF	chr19:42309840-42309990	MCF-7	breast:	n/a	chr19:42309918-42309931
3	CTCF	chr19:42309820-42309970	MCF-7	breast:	n/a	chr19:42309918-42309931
4	FOS	chr19:42308510-42308710	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr19:42308320-42308390	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYC	chr19:42308289-42308317	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:42308508-42308578	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr19:42308244-42308764	Raji	blood:	n/a	n/a
9	SPI1	chr19:42308395-42308779	HL-60	blood:	n/a	n/a
10	SRF	chr19:42308423-42308705	GM12878	blood:	n/a	chr19:42308578-42308596 chr19:42308582-42308593 chr19:42308583-42308592 chr19:42308581-42308594 chr19:42308578-42308592 chr19:42308581-42308594 chr19:42308576-42308593 chr19:42308579-42308596
11	STAT3	chr19:42308402-42308679	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr19:42308408-42308702	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr19:42308456-42308725	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42295737..42298028-chr19:42304935..42307847,2	MCF-7	breast:
2	chr19:42307703..42310642-chr19:42313204..42315165,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DMRTC2-2	chr19:42311149-42311655	NR_102333

Variant related genes	Relation type
CEACAM3	TF binding region

Extended variants
information (count: 176 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:176 , 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	rs587701960	chr19:42307682-42307683	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs587750875	chr19:42307716-42307717	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs587638335	chr19:42307730-42307731	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs587691515	chr19:42307731-42307732	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs587626752	chr19:42307796-42307797	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs587753073	chr19:42307797-42307798	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs367877157	chr19:42307798-42307799	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs13345108	chr19:42307805-42307806	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs185355141	chr19:42307842-42307843	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs573458281	chr19:42307845-42307846	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs76244989	chr19:42307849-42307850	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs368454176	chr19:42307877-42307878	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs562292023	chr19:42307917-42307918	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs529356032	chr19:42307921-42307922	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs550808022	chr19:42307925-42307926	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs199565597	chr19:42307960-42307961	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs562856773	chr19:42307979-42307980	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs372798480	chr19:42307993-42307994	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs111420627	chr19:42308030-42308031	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs10426020	chr19:42308031-42308032	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs10425474	chr19:42308034-42308035	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs10426049	chr19:42308080-42308081	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs112219122	chr19:42308082-42308083	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs548732560	chr19:42308101-42308102	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs560733370	chr19:42308124-42308125	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs79777880	chr19:42308125-42308126	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs10426243	chr19:42308145-42308146	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs10401370	chr19:42308164-42308165	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs10401528	chr19:42308183-42308184	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs117457389	chr19:42308237-42308238	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs191716900	chr19:42308243-42308244	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs577933949	chr19:42308265-42308266	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs558465674	chr19:42308266-42308267	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs8113283	chr19:42308287-42308288	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs540945120	chr19:42308306-42308307	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs77021364	chr19:42308310-42308311	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs10550157	chr19:42308324-42308325	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs76708165	chr19:42308325-42308326	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs75369233	chr19:42308362-42308363	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs562721474	chr19:42308393-42308394	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs138045517	chr19:42308400-42308401	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs183851152	chr19:42308415-42308416	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs543647719	chr19:42308423-42308424	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs188234512	chr19:42308438-42308439	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs8113720	chr19:42308440-42308441	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs527540855	chr19:42308459-42308460	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs548868210	chr19:42308485-42308486	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs8113538	chr19:42308500-42308501	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs537683184	chr19:42308525-42308526	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs8113813	chr19:42308535-42308536	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:64)

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
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
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
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	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
Genital abnormality	22378287	CNVD
Hypospadia	22378287	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Astrocytoma	22246337	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42304800-42316800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr19:42305000-42309000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:42305000-42310000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr19:42305200-42308800	Enhancers	Primary B cells from peripheral blood	blood
5	chr19:42305600-42308200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:42305800-42308200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr19:42307000-42308400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:42307000-42313600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:42307000-42314600	Weak transcription	Fetal Thymus	thymus
10	chr19:42307200-42308200	Weak transcription	GM12878-XiMat	blood
11	chr19:42307200-42309200	Enhancers	Primary hematopoietic stem cells	blood
12	chr19:42307200-42310000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr19:42307400-42307800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr19:42307400-42307800	Weak transcription	Primary B cells from cord blood	blood
15	chr19:42307800-42309600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr19:42307800-42310200	Enhancers	Primary B cells from cord blood	blood
17	chr19:42308200-42308400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:42308200-42308800	Enhancers	GM12878-XiMat	blood
19	chr19:42308200-42309000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr19:42308200-42309000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr19:42308200-42309200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr19:42308400-42308600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:42308400-42308600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:42308600-42308800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:42308800-42310200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:42308800-42313000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr19:42308800-42314400	Weak transcription	GM12878-XiMat	blood
28	chr19:42309000-42312000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:42309200-42312200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:42309600-42310600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
31	chr19:42310000-42311400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr19:42310000-42312000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr19:42310200-42311400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:42310200-42311800	Weak transcription	Primary B cells from cord blood	blood
35	chr19:42310400-42310600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:42310600-42311400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
37	chr19:42310600-42317800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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