Variant report

Variant	rs7257247
Chromosome Location	chr19:19755217-19755218
allele	A/G
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	POLR2A	chr19:19753227-19755267	GM12878	blood:	n/a	n/a
3	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
4	MXI1	chr19:19753469-19755349	IMR90	lung:	n/a	chr19:19754710-19754719
5	POLR2A	chr19:19753878-19755265	PFSK-1	brain:	n/a	n/a
6	TCF12	chr19:19754591-19755256	A549	lung:	n/a	n/a
7	CTCF	chr19:19755100-19755250	AG04449	skin:	n/a	n/a
8	POLR2A	chr19:19753156-19755303	GM12891	blood:	n/a	n/a
9	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
10	RAD21	chr19:19754009-19755238	HCT-116	colon:	n/a	chr19:19754824-19754837 chr19:19754825-19754835 chr19:19754963-19754976 chr19:19754821-19754840
11	POLR2A	chr19:19755096-19755433	K562	blood:	n/a	n/a
12	CTCF	chr19:19755160-19755310	HEK293	kidney:	n/a	n/a
13	POLR2A	chr19:19754077-19755394	MCF-7	breast:	n/a	n/a
14	POLR2A	chr19:19754144-19755351	SK-N-SH	brain:	n/a	n/a
15	SMC3	chr19:19753504-19755369	SK-N-SH	brain:	n/a	chr19:19754825-19754839 chr19:19754825-19754835
16	CTCF	chr19:19755080-19755230	GM12865	blood:	n/a	n/a
17	POLR2A	chr19:19753245-19755403	HL-60	blood:	n/a	n/a
18	POLR2A	chr19:19753773-19755260	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr19:19754221-19755352	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr19:19753708-19755255	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr19:19754210-19755622	HepG2	liver:	n/a	n/a
22	CTCF	chr19:19755120-19755270	WI-38	lung:	n/a	n/a
23	POLR2A	chr19:19753387-19755619	K562	blood:	n/a	n/a
24	CTCF	chr19:19755180-19755330	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr19:19754168-19755446	PFSK-1	brain:	n/a	n/a
26	MTA3	chr19:19752998-19755384	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:19754427-19755231	HepG2	liver:	n/a	n/a

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
ENSG00000178093	Chromatin interaction
ENSG00000250067	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000181896	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000089639	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11878966	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs11879251	1.00[EUR][1000 genomes]
rs11880104	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs11882164	1.00[EUR][1000 genomes]
rs11883102	1.00[EUR][1000 genomes]
rs17378427	1.00[EUR][1000 genomes]
rs34087491	1.00[EUR][1000 genomes]
rs57474361	1.00[EUR][1000 genomes]
rs58294398	1.00[EUR][1000 genomes]
rs60101043	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60133934	1.00[EUR][1000 genomes]
rs60610603	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61489113	1.00[EUR][1000 genomes]
rs7247366	1.00[EUR][1000 genomes]
rs7248802	1.00[EUR][1000 genomes]
rs7250144	1.00[EUR][1000 genomes]
rs7253515	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258865	1.00[EUR][1000 genomes]
rs73537247	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73537262	1.00[EUR][1000 genomes]
rs73537266	1.00[EUR][1000 genomes]
rs73539233	1.00[EUR][1000 genomes]
rs73539261	1.00[EUR][1000 genomes]
rs73541334	1.00[EUR][1000 genomes]
rs73541344	1.00[EUR][1000 genomes]
rs73541360	1.00[EUR][1000 genomes]
rs73541377	1.00[EUR][1000 genomes]
rs8105557	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111841	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8112744	1.00[EUR][1000 genomes]
rs8113100	1.00[EUR][1000 genomes]
rs9676945	1.00[EUR][1000 genomes]

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	chr19:19754600-19756000	Weak transcription	Gastric	stomach
3	chr19:19754800-19755400	Weak transcription	Osteobl	bone
4	chr19:19754800-19755600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:19754800-19755600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:19754800-19755600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:19754800-19755600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr19:19754800-19755600	Weak transcription	A549	lung
9	chr19:19754800-19755600	Weak transcription	NHLF	lung
10	chr19:19754800-19755800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:19754800-19755800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:19754800-19755800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:19754800-19755800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:19754800-19755800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:19754800-19755800	Weak transcription	Esophagus	oesophagus
16	chr19:19754800-19755800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:19754800-19755800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr19:19754800-19755800	Weak transcription	HUVEC	blood vessel
19	chr19:19754800-19756000	Weak transcription	Left Ventricle	heart
20	chr19:19754800-19756000	Weak transcription	Lung	lung
21	chr19:19754800-19756000	Weak transcription	Ovary	ovary
22	chr19:19754800-19756000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:19754800-19756200	Weak transcription	Aorta	Aorta
24	chr19:19754800-19756200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:19754800-19756400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:19754800-19756400	Weak transcription	Psoas Muscle	Psoas
27	chr19:19754800-19756400	Weak transcription	HMEC	breast
28	chr19:19754800-19756400	Weak transcription	HSMMtube	muscle
29	chr19:19754800-19756600	Weak transcription	Brain Substantia Nigra	brain
30	chr19:19754800-19757600	Weak transcription	NH-A	brain
31	chr19:19754800-19757800	Weak transcription	NHDF-Ad	bronchial
32	chr19:19754800-19761400	Weak transcription	HSMM	muscle
33	chr19:19754800-19763600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr19:19754800-19764200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:19754800-19767200	Weak transcription	Fetal Brain Male	brain
36	chr19:19754800-19769000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:19754800-19772400	Weak transcription	Right Atrium	heart
38	chr19:19755000-19755400	Enhancers	Primary B cells from cord blood	blood
39	chr19:19755000-19755400	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr19:19755000-19755400	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr19:19755000-19755400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:19755000-19755400	Genic enhancers	Rectal Mucosa Donor 29	rectum
43	chr19:19755000-19755400	Genic enhancers	Thymus	Thymus
44	chr19:19755000-19755600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr19:19755000-19755600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:19755000-19755600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:19755000-19755600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr19:19755000-19755800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr19:19755000-19756000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:19755000-19756000	Weak transcription	Colonic Mucosa	Colon

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