Variant report

Variant	rs549344474
Chromosome Location	chr19:42745789-42745790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr19:42745683-42745864	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:42745774-42746441	HCT-116	colon:	n/a	n/a
3	BCL3	chr19:42745641-42746557	A549	lung:	n/a	n/a
4	POLR2A	chr19:42745743-42747917	A549	lung:	n/a	n/a
5	JUN	chr19:42745677-42748054	K562	blood:	n/a	n/a
6	MXI1	chr19:42745522-42748046	IMR90	lung:	n/a	n/a
7	MXI1	chr19:42745370-42749605	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr19:42745686-42752051	A549	lung:	n/a	n/a
9	POLR2A	chr19:42745562-42745790	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:42745784-42747882	PBDE	blood:	n/a	n/a
11	POLR2A	chr19:42745487-42746183	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:42743213-42746291	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr19:42745625-42747824	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr19:42745727-42755683	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr19:42745606-42747873	MCF10A-Er-Src	breast:	n/a	n/a
16	CTCF	chr19:42745325-42749655	A549	lung:	n/a	n/a
17	ESRRA	chr19:42745657-42747767	GM12878	blood:	n/a	chr19:42746224-42746243 chr19:42746231-42746244 chr19:42746006-42746016 chr19:42746232-42746244
18	POLR2A	chr19:42745596-42747910	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42719158..42725942-chr19:42744280..42751391,14	MCF-7	breast:
2	chr19:42722142..42727268-chr19:42743805..42748670,12	MCF-7	breast:
3	chr19:42745106..42750336-chr19:42827948..42831181,5	K562	blood:
4	chr19:42634611..42641780-chr19:42741001..42747645,8	MCF-7	breast:
5	chr11:1855536..1857574-chr19:42743518..42745995,2	MCF-7	breast:
6	chr19:42744952..42747031-chr19:42828094..42829861,2	MCF-7	breast:
7	chr19:42745670..42748955-chr19:42805967..42808847,6	K562	blood:
8	chr19:42745106..42746807-chr19:42829655..42831181,2	K562	blood:
9	chr19:42745110..42750037-chr19:42804255..42809210,7	MCF-7	breast:
10	chr19:42744297..42761073-chr19:42776978..42802286,113	MCF-7	breast:
11	chr19:42720291..42721967-chr19:42744668..42747834,3	MCF-7	breast:
12	chr19:42734779..42737067-chr19:42745327..42747787,2	MCF-7	breast:
13	chr19:42745751..42747885-chr19:42828050..42829792,2	MCF-7	breast:
14	chr19:42743599..42762610-chr19:42780302..42801550,102	MCF-7	breast:
15	chr19:42695805..42698002-chr19:42744697..42747110,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000204957	TF binding region
ENSG00000160570	Chromatin interaction
ENSG00000105723	Chromatin interaction
ENSG00000266226	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000188368	Chromatin interaction
ENSG00000167625	Chromatin interaction
ENSG00000149043	Chromatin interaction
ENSG00000028277	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000254887	Chromatin interaction
ENSG00000265122	Chromatin interaction
ENSG00000105429	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
9	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
11	nsv911784	chr19:42741124-42787664	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
12	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
13	nsv911786	chr19:42744234-42797959	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	39 gene(s)	inside rSNPs	diseases
14	esv3352699	chr19:42745662-42747910	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42725000-42747000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:42741000-42745800	Weak transcription	Aorta	Aorta
3	chr19:42741200-42745800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:42744200-42745800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:42744400-42745800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:42744400-42745800	Weak transcription	Lung	lung
7	chr19:42744400-42745800	Enhancers	Pancreas	Pancrea
8	chr19:42744600-42745800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr19:42744600-42745800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr19:42744600-42745800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:42744600-42745800	Weak transcription	Ovary	ovary
12	chr19:42744600-42746000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:42744600-42748800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:42744800-42745800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:42744800-42745800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr19:42744800-42745800	Enhancers	Primary B cells from peripheral blood	blood
17	chr19:42744800-42745800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr19:42744800-42745800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:42744800-42745800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:42744800-42745800	Enhancers	Brain Substantia Nigra	brain
21	chr19:42744800-42745800	Weak transcription	Esophagus	oesophagus
22	chr19:42744800-42745800	Transcr. at gene 5' and 3'	A549	lung
23	chr19:42744800-42746000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:42744800-42746200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr19:42745000-42745800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr19:42745000-42745800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:42745000-42745800	Weak transcription	Gastric	stomach
28	chr19:42745000-42745800	Enhancers	Left Ventricle	heart
29	chr19:42745000-42745800	Transcr. at gene 5' and 3'	K562	blood
30	chr19:42745000-42748000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:42745200-42745800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:42745200-42745800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr19:42745200-42745800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:42745200-42745800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:42745200-42748200	Active TSS	HSMM	muscle
36	chr19:42745400-42745800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:42745400-42745800	Flanking Active TSS	Stomach Mucosa	stomach
38	chr19:42745400-42745800	Flanking Active TSS	HepG2	liver
39	chr19:42745400-42746000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:42745400-42746000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:42745400-42746000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:42745400-42746000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr19:42745400-42746000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr19:42745400-42746000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:42745400-42746000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:42745400-42746000	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr19:42745400-42746000	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr19:42745400-42746000	Flanking Active TSS	GM12878-XiMat	blood
49	chr19:42745400-42746000	Flanking Active TSS	HMEC	breast
50	chr19:42745400-42746000	Flanking Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links