Variant report

Variant	rs599859
Chromosome Location	chr19:53088116-53088117
allele	A/C/T
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	chr19:53088097-53088275	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:53073504..53075016-chr19:53086712..53089202,2	MCF-7	breast:
2	chr19:53087080..53089827-chr19:53090383..53092275,2	K562	blood:
3	chr19:53086321..53088746-chr19:53090945..53093130,2	K562	blood:

Variant related genes	Relation type
ZNF137P	TF binding region
ENSG00000123870	Chromatin interaction
ENSG00000167562	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs368683	0.98[ASN][1000 genomes]
rs369009	1.00[ASN][1000 genomes]
rs374395	0.98[ASN][1000 genomes]
rs544769	0.98[ASN][1000 genomes]
rs544869	0.82[ASN][1000 genomes]
rs650750	0.98[ASN][1000 genomes]
rs661876	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv912304	chr19:53071155-53114267	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv3385321	chr19:53086990-53090388	ZNF genes & repeats Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53074600-53103600	Weak transcription	Fetal Brain Male	brain
2	chr19:53075400-53089600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:53075400-53092200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:53075400-53092400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:53075400-53092400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:53076400-53096000	Strong transcription	Dnd41	blood
7	chr19:53079200-53092200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:53079400-53089400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr19:53079400-53090400	ZNF genes & repeats	Liver	Liver
10	chr19:53079400-53092200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
11	chr19:53079400-53094200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:53079400-53096000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:53079600-53089600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:53079600-53091800	ZNF genes & repeats	Thymus	Thymus
15	chr19:53079800-53089200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:53079800-53091000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:53080200-53089400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:53081600-53088400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:53081600-53090200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
20	chr19:53082200-53089200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
21	chr19:53082800-53089200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
22	chr19:53083200-53091000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:53083400-53088800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
24	chr19:53083400-53089200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
25	chr19:53083400-53090400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
26	chr19:53083400-53091000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:53083600-53088400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:53083600-53088600	ZNF genes & repeats	Primary T cells from cord blood	blood
29	chr19:53083600-53088600	ZNF genes & repeats	GM12878-XiMat	blood
30	chr19:53083600-53090400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:53083600-53090800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
32	chr19:53083600-53092400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:53083800-53088600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr19:53083800-53092400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
35	chr19:53084600-53091200	ZNF genes & repeats	Colonic Mucosa	Colon
36	chr19:53084800-53088200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr19:53084800-53088200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:53084800-53088400	ZNF genes & repeats	HMEC	breast
39	chr19:53085000-53088200	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr19:53085400-53088200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:53085400-53089200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:53085400-53089200	ZNF genes & repeats	NHEK	skin
43	chr19:53085400-53091200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:53085800-53088600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:53085800-53089200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:53086400-53088200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr19:53086800-53090000	ZNF genes & repeats	Lung	lung
48	chr19:53087000-53088400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr19:53087200-53088800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr19:53087200-53091000	ZNF genes & repeats	Spleen	Spleen

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