Variant report

Variant	esv3342196
Chromosome Location	chr19:42653537-42656085
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	chr19:42654180-42654330	HepG2	liver:	n/a	chr19:42654221-42654239 chr19:42654227-42654236
2	CTCF	chr19:42653880-42654030	A549	lung:	n/a	n/a
3	CTCF	chr19:42653860-42654010	A549	lung:	n/a	n/a
4	CTCF	chr19:42653919-42653927	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr19:42654140-42654290	A549	lung:	n/a	chr19:42654221-42654239 chr19:42654227-42654236
6	CTCF	chr19:42654160-42654310	GM12873	blood:	n/a	chr19:42654221-42654239 chr19:42654227-42654236
7	CTCF	chr19:42653936-42653991	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr19:42654160-42654310	WERI-Rb-1	eye:	n/a	chr19:42654221-42654239 chr19:42654227-42654236
9	CTCF	chr19:42654160-42654310	HEK293	kidney:	n/a	chr19:42654221-42654239 chr19:42654227-42654236
10	CTCF	chr19:42654230-42654269	MCF-7	breast:	n/a	n/a
11	CTCF	chr19:42654080-42654230	SAEC	small airway:	n/a	n/a
12	CTCF	chr19:42654276-42654291	MCF-7	breast:	n/a	n/a
13	CTCF	chr19:42654191-42654301	H1-hESC	embryonic stem cell:	n/a	chr19:42654221-42654239 chr19:42654227-42654236
14	EBF1	chr19:42653588-42653882	GM12878	blood:	n/a	chr19:42653723-42653734
15	POLR2A	chr19:42655799-42655824	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr19:42656018-42656037	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr19:42655888-42655898	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr19:42655166-42655229	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42652766..42655502-chr19:42672644..42674234,2	MCF-7	breast:
2	chr19:42650733..42654783-chr19:42655622..42659821,6	K562	blood:
3	chr19:42637467..42639958-chr19:42655393..42657223,2	K562	blood:

Variant related genes	Relation type
ENSG00000259436	TF binding region
ENSG00000259436	chromatin interactions
ENSG00000254887	chromatin interactions
ENSG00000266226	chromatin interactions

Extended variants
information (count: 79 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:79 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs544755214	chr19:42653559-42653560	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs187001636	chr19:42653584-42653585	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs147753009	chr19:42653654-42653655	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs545047410	chr19:42653751-42653752	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs560414203	chr19:42653782-42653783	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs376555624	chr19:42653807-42653808	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs572630359	chr19:42653808-42653809	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs527616839	chr19:42653895-42653896	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs548847471	chr19:42653921-42653922	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs567170988	chr19:42653928-42653929	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs531394026	chr19:42653934-42653935	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs549858832	chr19:42653939-42653940	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs190812765	chr19:42653954-42653955	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs113697072	chr19:42653965-42653966	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs141078768	chr19:42653982-42653983	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs149830743	chr19:42653983-42653984	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs565657083	chr19:42653999-42654000	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs11880214	chr19:42654002-42654003	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs182995676	chr19:42654049-42654050	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs556083829	chr19:42654067-42654068	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs574291119	chr19:42654090-42654091	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs80334885	chr19:42654098-42654099	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs537571310	chr19:42654109-42654110	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs369156712	chr19:42654201-42654202	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs556641987	chr19:42654277-42654278	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs578009967	chr19:42654363-42654364	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs545471429	chr19:42654379-42654380	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs560315696	chr19:42654390-42654391	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs71361004	chr19:42654438-42654439	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs148956700	chr19:42654441-42654442	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs115123972	chr19:42654442-42654443	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs560809345	chr19:42654443-42654444	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs145731795	chr19:42654471-42654472	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs71361005	chr19:42654502-42654503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs73932874	chr19:42654555-42654556	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs565074819	chr19:42654699-42654700	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs191699156	chr19:42654750-42654751	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs182851837	chr19:42654760-42654761	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs545084655	chr19:42654791-42654792	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs113232113	chr19:42654905-42654906	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs114699142	chr19:42654923-42654924	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs138313110	chr19:42654942-42654943	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs113496381	chr19:42654953-42654954	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs549699228	chr19:42654975-42654976	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs567930427	chr19:42654984-42654985	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs538450057	chr19:42655104-42655105	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs556516725	chr19:42655166-42655167	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs141244775	chr19:42655209-42655210	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs73552838	chr19:42655210-42655211	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs553840935	chr19:42655217-42655218	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a

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
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42637600-42658200	Weak transcription	Right Atrium	heart
2	chr19:42640200-42659400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:42642800-42653800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:42643200-42654000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:42644600-42653800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:42649800-42653800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr19:42651400-42653800	Weak transcription	Fetal Brain Female	brain
8	chr19:42651800-42653600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:42651800-42653800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr19:42652000-42653800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr19:42652000-42654400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr19:42652000-42654400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr19:42652000-42654400	Bivalent Enhancer	Fetal Thymus	thymus
14	chr19:42652200-42653800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr19:42652200-42654200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr19:42652400-42653600	Enhancers	Thymus	Thymus
17	chr19:42652600-42658800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:42652800-42653800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:42653000-42653600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:42653000-42654000	Enhancers	Brain Germinal Matrix	brain
21	chr19:42653000-42654000	Bivalent Enhancer	NHEK	skin
22	chr19:42653000-42654400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:42653000-42656000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:42653200-42653600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr19:42653200-42653600	Bivalent Enhancer	Esophagus	oesophagus
26	chr19:42653200-42654000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:42653200-42654400	Enhancers	H9 Cell Line	embryonic stem cell
28	chr19:42653200-42655000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:42653200-42661200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:42653400-42654200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
31	chr19:42653400-42654200	Enhancers	Primary B cells from cord blood	blood
32	chr19:42653400-42654400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
33	chr19:42653400-42654400	Enhancers	Primary T cells from cord blood	blood
34	chr19:42653400-42655800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr19:42653400-42656400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr19:42653600-42654200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:42653600-42654400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
38	chr19:42653600-42655800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr19:42653600-42656400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr19:42653600-42659000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr19:42653800-42654000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
42	chr19:42653800-42654000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:42653800-42654200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
44	chr19:42653800-42654200	Enhancers	Primary B cells from peripheral blood	blood
45	chr19:42653800-42654200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:42653800-42654200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:42653800-42654400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
48	chr19:42653800-42656400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:42653800-42657400	Enhancers	Fetal Brain Female	brain
50	chr19:42653800-42658000	Enhancers	Pancreas	Pancrea

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