Variant report

Variant	rs1048552
Chromosome Location	chr19:45666234-45666235
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:45666013-45666275	MCF-7	breast:	n/a	n/a
2	POLR2A	chr19:45666159-45666667	K562	blood:	n/a	n/a
3	POLR2A	chr19:45666228-45666235	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45646729..45650244-chr19:45666195..45669472,3	MCF-7	breast:
2	chr19:45664293..45670548-chr19:45677917..45684715,10	MCF-7	breast:
3	chr19:45663965..45672033-chr19:45672145..45675901,9	K562	blood:
4	chr19:45664265..45666960-chr19:45670245..45671965,2	K562	blood:
5	chr19:45664797..45666644-chr19:45690247..45693088,2	K562	blood:
6	chr19:45664074..45668689-chr19:45680998..45684242,7	MCF-7	breast:
7	chr19:45558584..45560889-chr19:45665988..45668898,2	K562	blood:
8	chr19:45665641..45668911-chr19:45670300..45671967,3	K562	blood:
9	chr19:45665456..45669944-chr19:45672662..45676859,4	MCF-7	breast:
10	chr19:45662322..45668242-chr19:45680645..45684470,7	K562	blood:

No data

Variant related genes	Relation type
NKPD1	TF binding region
ENSG00000189114	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000266958	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000267545	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12459817	1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12460178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12461733	1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12463298	0.83[AMR][1000 genomes]
rs12463327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57302271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57627123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58504789	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59215448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60460304	1.00[AMR][1000 genomes]
rs6509200	0.85[AFR][1000 genomes]
rs73564216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564218	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1798099	chr19:45664218-45681988	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45657800-45668200	Weak transcription	Right Atrium	heart
2	chr19:45660200-45674000	Weak transcription	A549	lung
3	chr19:45662000-45667000	Weak transcription	Spleen	Spleen
4	chr19:45662400-45667200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr19:45662600-45666600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr19:45662600-45667600	Weak transcription	HUVEC	blood vessel
7	chr19:45662800-45669000	Enhancers	Esophagus	oesophagus
8	chr19:45664000-45666400	Bivalent Enhancer	Colonic Mucosa	Colon
9	chr19:45664000-45667600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:45664000-45670200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:45664200-45667800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:45664200-45668400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:45664600-45667600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:45664800-45666400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr19:45664800-45666800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr19:45665000-45666400	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr19:45665000-45667600	Weak transcription	Gastric	stomach
18	chr19:45665000-45667600	Weak transcription	Pancreas	Pancrea
19	chr19:45665400-45666800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:45665400-45667200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:45665400-45667400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:45665400-45667400	Weak transcription	Ovary	ovary
23	chr19:45665400-45667600	Weak transcription	Lung	lung
24	chr19:45665400-45669800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:45665400-45670000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:45665400-45670200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr19:45665400-45680400	Weak transcription	Brain Substantia Nigra	brain
28	chr19:45665400-45680600	Weak transcription	Fetal Lung	lung
29	chr19:45665600-45666400	Weak transcription	Right Ventricle	heart
30	chr19:45665600-45666600	Flanking Active TSS	NHEK	skin
31	chr19:45665600-45667800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:45665600-45680400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr19:45665800-45674600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:45665800-45680200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:45665800-45680400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:45666000-45666600	Weak transcription	Brain Hippocampus Middle	brain
37	chr19:45666000-45667000	Weak transcription	Placenta	Placenta
38	chr19:45666000-45668000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr19:45666000-45669200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr19:45666000-45669200	Enhancers	HMEC	breast
41	chr19:45666000-45669800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr19:45666200-45666400	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr19:45666200-45666400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:45666200-45666600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr19:45666200-45667200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:45666200-45667400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:45666200-45667600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:45666200-45668800	Enhancers	Placenta Amnion	Placenta Amnion

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