Variant report

Variant	esv3406716
Chromosome Location	chr19:51477740-51479638
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	ELF1	chr19:51478984-51479505	MCF-7	breast:	n/a	chr19:51479159-51479170
2	ELF1	chr19:51478988-51479507	MCF-7	breast:	n/a	chr19:51479159-51479170
3	EP300	chr19:51478920-51479337	MCF-7	breast:	n/a	n/a
4	FOS	chr19:51479130-51479340	MCF10A-Er-Src	breast:	n/a	chr19:51479281-51479289
5	FOSL2	chr19:51479021-51479531	MCF-7	breast:	n/a	chr19:51479281-51479289
6	GATA3	chr19:51478977-51479476	MCF-7	breast:	n/a	chr19:51479102-51479114 chr19:51479103-51479113 chr19:51479105-51479112
7	GATA3	chr19:51478906-51479582	MCF-7	breast:	n/a	chr19:51479102-51479114 chr19:51479103-51479113 chr19:51479105-51479112
8	GATA3	chr19:51478930-51479709	MCF-7	breast:	n/a	chr19:51479102-51479114 chr19:51479103-51479113 chr19:51479105-51479112
9	HDAC2	chr19:51478973-51479440	MCF-7	breast:	n/a	chr19:51479104-51479113 chr19:51479377-51479386
10	JUND	chr19:51478881-51479746	HCT-116	colon:	n/a	chr19:51479281-51479289
11	MAX	chr19:51478951-51479584	MCF-7	breast:	n/a	n/a
12	MYC	chr19:51479221-51479276	MCF-7	breast:	n/a	n/a
13	MYC	chr19:51479109-51479318	MCF-7	breast:	n/a	n/a
14	MYC	chr19:51479285-51479379	MCF-7	breast:	n/a	n/a
15	POLR2A	chr19:51479160-51479386	MCF-7	breast:	n/a	n/a
16	POLR2A	chr19:51479141-51479508	MCF-7	breast:	n/a	n/a
17	POLR2A	chr19:51478955-51479750	HCT-116	colon:	n/a	n/a
18	POLR2A	chr19:51479271-51479392	MCF-7	breast:	n/a	n/a
19	POLR2A	chr19:51478865-51479644	HCT-116	colon:	n/a	n/a
20	POLR2A	chr19:51479486-51479553	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr19:51479527-51479530	Gliobla	brain:	n/a	n/a
22	POLR2A	chr19:51479388-51479491	Gliobla	brain:	n/a	n/a
23	POLR2A	chr19:51479266-51479267	MCF-7	breast:	n/a	n/a
24	SIN3AK20	chr19:51478936-51479655	MCF-7	breast:	n/a	n/a
25	SP1	chr19:51478909-51479660	HCT-116	colon:	n/a	n/a
26	SP1	chr19:51478907-51479925	HCT-116	colon:	n/a	n/a
27	TCF7L2	chr19:51479037-51479697	HCT-116	colon:	n/a	chr19:51479242-51479256 chr19:51479245-51479254
28	TCF7L2	chr19:51479045-51479483	Hela-S3	cervix:	n/a	chr19:51479242-51479256 chr19:51479245-51479254
29	TCF7L2	chr19:51478997-51479532	MCF-7	breast:	n/a	chr19:51479242-51479256 chr19:51479245-51479254
30	YY1	chr19:51478971-51479462	HCT-116	colon:	n/a	n/a
31	ZNF143	chr19:51479048-51479626	H1-hESC	embryonic stem cell:	n/a	chr19:51479141-51479160
32	ZNF217	chr19:51478981-51479445	MCF-7	breast:	n/a	n/a
33	ZNF263	chr19:51479141-51479608	HEK293-T-REx	kidney:	n/a	chr19:51479295-51479304

No.	Distal block	Cell Line	Cell type
1	chr19:51470577..51473158-chr19:51478017..51482058,3	K562	blood:
2	chr19:51432732..51437222-chr19:51477627..51480793,4	MCF-7	breast:
3	chr19:51473357..51476193-chr19:51479340..51481047,2	K562	blood:
4	chr19:51474799..51477178-chr19:51477869..51480485,2	MCF-7	breast:
5	chr19:51474380..51475999-chr19:51476075..51479052,2	MCF-7	breast:
6	chr19:51470577..51472254-chr19:51478017..51480801,2	K562	blood:
7	chr19:51478311..51481235-chr19:51486537..51488716,3	MCF-7	breast:

Variant related genes	Relation type
KLK6	TF binding region
ENSG00000169035	chromatin interactions
ENSG00000167755	chromatin interactions
ENSG00000267879	chromatin interactions

Extended variants
information (count: 64 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:64 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs112290835	chr19:51477749-51477750	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
2	rs532437033	chr19:51477793-51477794	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
3	rs550974657	chr19:51477795-51477796	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
4	rs535088816	chr19:51477831-51477832	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs553321250	chr19:51477863-51477864	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs143447830	chr19:51477865-51477866	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs57889828	chr19:51478000-51478001	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs397761829	chr19:51478002-51478003	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs77449988	chr19:51478003-51478004	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs549209303	chr19:51478044-51478045	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs370748453	chr19:51478047-51478048	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs539327960	chr19:51478075-51478076	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs567303530	chr19:51478076-51478077	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs186085740	chr19:51478094-51478095	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs534814318	chr19:51478107-51478108	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs191004992	chr19:51478118-51478119	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs12151293	chr19:51478283-51478284	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs200101404	chr19:51478288-51478289	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs28621774	chr19:51478291-51478292	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs556385180	chr19:51478339-51478340	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs187910133	chr19:51478386-51478387	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs12978297	chr19:51478410-51478411	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs12978337	chr19:51478453-51478454	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs12979717	chr19:51478456-51478457	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs191994252	chr19:51478462-51478463	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs12978369	chr19:51478493-51478494	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs10420260	chr19:51478497-51478498	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs571304964	chr19:51478498-51478499	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs538275383	chr19:51478500-51478501	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs12151304	chr19:51478506-51478507	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs12151308	chr19:51478545-51478546	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs12151087	chr19:51478547-51478548	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs556507695	chr19:51478553-51478554	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs575545809	chr19:51478627-51478628	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs111219882	chr19:51478631-51478632	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs71185783	chr19:51478658-51478659	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs560484722	chr19:51478739-51478740	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs528024659	chr19:51478741-51478742	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs12978725	chr19:51478797-51478798	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs546509312	chr19:51478832-51478833	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs77273360	chr19:51478837-51478838	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs564746945	chr19:51478867-51478868	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs374968245	chr19:51478905-51478906	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs188159283	chr19:51478911-51478912	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs71185784	chr19:51478948-51478949	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs372219368	chr19:51478949-51478950	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs376741639	chr19:51478952-51478953	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs542870665	chr19:51478954-51478955	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs555146160	chr19:51478995-51478996	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs573400330	chr19:51479001-51479002	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:59)

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
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	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
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian cancer	22174824	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Wilms tumour	21544195	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	18852474	CNVD
Glioblastoma multiforme	17002787	CNVD
Cervical cancer	21062161	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	16573809	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Adrenocortical carcinoma	18281524	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51472800-51482200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr19:51473000-51480600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:51473200-51479000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:51473200-51479000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:51473200-51480800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:51473200-51482400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:51473800-51479000	Weak transcription	NHEK	skin
8	chr19:51474800-51479000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:51474800-51479000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr19:51474800-51482200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:51476200-51477800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr19:51476200-51479000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:51476400-51479000	Weak transcription	HMEC	breast
14	chr19:51476600-51479000	Weak transcription	Esophagus	oesophagus
15	chr19:51477400-51478000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr19:51477400-51479200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:51477600-51477800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:51477600-51478000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr19:51477800-51479200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:51478000-51479000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:51478000-51479000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:51479000-51479400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr19:51479000-51479400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:51479000-51479400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:51479000-51479400	Bivalent Enhancer	A549	lung
26	chr19:51479000-51479600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr19:51479000-51479600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr19:51479000-51479600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr19:51479000-51479600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:51479000-51479600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:51479000-51479600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:51479000-51479600	Enhancers	Esophagus	oesophagus
33	chr19:51479000-51479600	Enhancers	NHEK	skin
34	chr19:51479000-51479800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr19:51479000-51480000	Enhancers	HMEC	breast
36	chr19:51479200-51479400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
37	chr19:51479200-51479600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:51479200-51479600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:51479200-51479600	Enhancers	Gastric	stomach
40	chr19:51479200-51479600	Bivalent Enhancer	Lung	lung
41	chr19:51479200-51479600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr19:51479400-51479600	Enhancers	H9 Cell Line	embryonic stem cell
43	chr19:51479400-51480800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr19:51479400-51481600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:51479400-51482200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:51479600-51480800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:51479600-51480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:51479600-51481000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr19:51479600-51481400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr19:51479600-51482000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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