Variant report

Variant	rs534810509
Chromosome Location	chr19:19755147-19755148
allele	A/C
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	POLR2A	chr19:19755119-19755264	GM12878	blood:	n/a	n/a
2	CTCF	chr19:19755141-19755172	K562	blood:	n/a	n/a
3	POLR2A	chr19:19753227-19755267	GM12878	blood:	n/a	n/a
4	ZBTB7A	chr19:19753864-19755188	ECC-1	luminal epithelium:	n/a	chr19:19754561-19754569 chr19:19754824-19754833 chr19:19754909-19754916
5	CTCF	chr19:19755093-19755150	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr19:19754395-19755223	A549	lung:	n/a	chr19:19754825-19754838 chr19:19754818-19754839 chr19:19754829-19754838 chr19:19754824-19754840 chr19:19754826-19754836 chr19:19754823-19754841 chr19:19754825-19754838
7	MXI1	chr19:19753469-19755349	IMR90	lung:	n/a	chr19:19754710-19754719
8	POLR2A	chr19:19753878-19755265	PFSK-1	brain:	n/a	n/a
9	CTCF	chr19:19755094-19755201	GM10266	blood:	n/a	n/a
10	TCF12	chr19:19754591-19755256	A549	lung:	n/a	n/a
11	CTCF	chr19:19755100-19755250	AG04449	skin:	n/a	n/a
12	POLR2A	chr19:19753156-19755303	GM12891	blood:	n/a	n/a
13	CTCF	chr19:19753978-19755460	SK-N-SH	brain:	n/a	chr19:19754825-19754838 chr19:19754818-19754839 chr19:19754829-19754838 chr19:19754824-19754840 chr19:19754826-19754836 chr19:19754823-19754841 chr19:19754825-19754838
14	RAD21	chr19:19754009-19755238	HCT-116	colon:	n/a	chr19:19754824-19754837 chr19:19754825-19754835 chr19:19754963-19754976 chr19:19754821-19754840
15	POLR2A	chr19:19755096-19755433	K562	blood:	n/a	n/a
16	POLR2A	chr19:19754051-19755199	U87	brain:	n/a	n/a
17	CTCF	chr19:19754342-19755206	HCT-116	colon:	n/a	chr19:19754825-19754838 chr19:19754818-19754839 chr19:19754829-19754838 chr19:19754824-19754840 chr19:19754826-19754836 chr19:19754823-19754841 chr19:19754825-19754838
18	POLR2A	chr19:19753995-19755186	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr19:19755020-19755170	GM12871	blood:	n/a	n/a
20	POLR2A	chr19:19754077-19755394	MCF-7	breast:	n/a	n/a
21	POLR2A	chr19:19754144-19755351	SK-N-SH	brain:	n/a	n/a
22	RAD21	chr19:19754141-19755194	HCT-116	colon:	n/a	chr19:19754824-19754837 chr19:19754825-19754835 chr19:19754963-19754976 chr19:19754821-19754840
23	SMC3	chr19:19753504-19755369	SK-N-SH	brain:	n/a	chr19:19754825-19754839 chr19:19754825-19754835
24	SMC3	chr19:19754483-19755193	GM12878	blood:	n/a	chr19:19754825-19754839 chr19:19754825-19754835
25	CTCF	chr19:19755080-19755230	GM12865	blood:	n/a	n/a
26	POLR2A	chr19:19753245-19755403	HL-60	blood:	n/a	n/a
27	POLR2A	chr19:19753773-19755260	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr19:19753277-19755150	HL-60	blood:	n/a	n/a
29	POLR2A	chr19:19754221-19755352	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr19:19754057-19755193	U87	brain:	n/a	n/a
31	POLR2A	chr19:19753708-19755255	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr19:19754210-19755622	HepG2	liver:	n/a	n/a
33	NFATC1	chr19:19754105-19755179	GM12878	blood:	n/a	n/a
34	CTCF	chr19:19755120-19755270	WI-38	lung:	n/a	n/a
35	POLR2A	chr19:19753387-19755619	K562	blood:	n/a	n/a
36	MXI1	chr19:19753050-19755147	SK-N-SH	brain:	n/a	chr19:19754710-19754719
37	POLR2A	chr19:19754168-19755446	PFSK-1	brain:	n/a	n/a
38	SMC3	chr19:19754642-19755160	HepG2	liver:	n/a	chr19:19754825-19754839 chr19:19754825-19754835
39	MTA3	chr19:19752998-19755384	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:19754427-19755231	HepG2	liver:	n/a	n/a
41	RAD21	chr19:19753178-19755189	SK-N-SH	brain:	n/a	chr19:19754824-19754837 chr19:19754825-19754835 chr19:19754963-19754976 chr19:19754821-19754840

No.	Distal block	Cell Line	Cell type
1	chr19:19751893..19756920-chr19:19758472..19762276,9	K562	blood:
2	chr19:19736821..19742043-chr19:19751528..19755876,8	MCF-7	breast:
3	chr19:19649879..19653588-chr19:19753029..19755939,4	K562	blood:
4	chr19:19751259..19758144-chr19:19770384..19776332,14	K562	blood:
5	chr19:19752450..19756333-chr19:19763709..19769200,7	K562	blood:
6	chr19:19753961..19756109-chr19:19770427..19773007,2	MCF-7	breast:
7	chr19:19753534..19755355-chr19:19771479..19774786,3	MCF-7	breast:
8	chr19:19746005..19749139-chr19:19754452..19756751,3	K562	blood:
9	chr19:19751259..19757786-chr19:19771999..19776232,8	K562	blood:
10	chr19:19752883..19756107-chr19:19759212..19764518,8	MCF-7	breast:
11	chr19:19625550..19627956-chr19:19752305..19756076,5	MCF-7	breast:
12	chr19:19752144..19756505-chr19:19773208..19775858,7	MCF-7	breast:
13	chr19:19635157..19637400-chr19:19754505..19756149,2	K562	blood:
14	chr19:19754487..19757148-chr19:19764604..19766993,2	K562	blood:
15	chr19:19637478..19643205-chr19:19752988..19755970,5	MCF-7	breast:
16	chr19:19754977..19756747-chr19:19789710..19792104,2	K562	blood:
17	chr19:19746514..19749043-chr19:19754284..19756520,2	MCF-7	breast:

Variant related genes	Relation type
GMIP	TF binding region
ENSG00000105726	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000250067	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000181896	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000089639	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv911310	chr19:19753882-19784891	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19754400-19755800	Weak transcription	Small Intestine	intestine
2	chr19:19754600-19755200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr19:19754600-19755200	Flanking Active TSS	GM12878-XiMat	blood
4	chr19:19754600-19756000	Weak transcription	Gastric	stomach
5	chr19:19754800-19755200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:19754800-19755200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:19754800-19755200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:19754800-19755200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:19754800-19755200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:19754800-19755200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:19754800-19755200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr19:19754800-19755200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:19754800-19755200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr19:19754800-19755200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr19:19754800-19755200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:19754800-19755200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:19754800-19755200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:19754800-19755200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr19:19754800-19755200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:19754800-19755200	Enhancers	Liver	Liver
21	chr19:19754800-19755200	Weak transcription	Brain Anterior Caudate	brain
22	chr19:19754800-19755200	Enhancers	Fetal Intestine Small	intestine
23	chr19:19754800-19755200	Enhancers	Fetal Kidney	kidney
24	chr19:19754800-19755200	Weak transcription	Fetal Lung	lung
25	chr19:19754800-19755200	Genic enhancers	Fetal Muscle Leg	muscle
26	chr19:19754800-19755200	Genic enhancers	Fetal Stomach	stomach
27	chr19:19754800-19755200	Enhancers	Right Ventricle	heart
28	chr19:19754800-19755200	Weak transcription	Spleen	Spleen
29	chr19:19754800-19755200	Weak transcription	NHEK	skin
30	chr19:19754800-19755400	Weak transcription	Osteobl	bone
31	chr19:19754800-19755600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr19:19754800-19755600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:19754800-19755600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:19754800-19755600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr19:19754800-19755600	Weak transcription	A549	lung
36	chr19:19754800-19755600	Weak transcription	NHLF	lung
37	chr19:19754800-19755800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:19754800-19755800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:19754800-19755800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr19:19754800-19755800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:19754800-19755800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:19754800-19755800	Weak transcription	Esophagus	oesophagus
43	chr19:19754800-19755800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr19:19754800-19755800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:19754800-19755800	Weak transcription	HUVEC	blood vessel
46	chr19:19754800-19756000	Weak transcription	Left Ventricle	heart
47	chr19:19754800-19756000	Weak transcription	Lung	lung
48	chr19:19754800-19756000	Weak transcription	Ovary	ovary
49	chr19:19754800-19756000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr19:19754800-19756200	Weak transcription	Aorta	Aorta

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