Variant report

Variant	rs565545
Chromosome Location	chr19:39895580-39895581
allele	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	SIN3AK20	chr19:39895490-39907815	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
3	ZNF384	chr19:39895573-39895773	K562	blood:	n/a	n/a
4	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:39895461-39895661	K562	blood:	n/a	n/a
6	POLR2A	chr19:39895363-39896989	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39615977..39618241-chr19:39893024..39896089,3	MCF-7	breast:
2	chr19:39893196..39895716-chr19:39934783..39936652,2	MCF-7	breast:

Variant related genes	Relation type
ZFP36	TF binding region
ENSG00000196235	Chromatin interaction
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10402122	0.93[AMR][1000 genomes]
rs10403504	0.91[AMR][1000 genomes]
rs10412877	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10414216	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10423565	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10425594	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11665856	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11672863	0.90[AMR][1000 genomes]
rs12973448	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12977767	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs251864	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3843755	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4803235	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7250966	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7253005	0.84[AMR][1000 genomes]
rs7256692	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
9	nsv911686	chr19:39891219-39907781	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	171 gene(s)	inside rSNPs	diseases
10	nsv911687	chr19:39891219-39909714	Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	171 gene(s)	inside rSNPs	diseases
11	nsv911688	chr19:39891219-39919538	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 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	chr19:39893200-39896800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr19:39893200-39897000	Weak transcription	Gastric	stomach
3	chr19:39893800-39896200	Weak transcription	Dnd41	blood
4	chr19:39894200-39896600	Weak transcription	HepG2	liver
5	chr19:39894200-39897000	Weak transcription	Ovary	ovary
6	chr19:39894200-39897000	Weak transcription	Pancreas	Pancrea
7	chr19:39894400-39896800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:39894400-39896800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:39894600-39896600	Enhancers	NHDF-Ad	bronchial
10	chr19:39894800-39895800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:39894800-39896400	Enhancers	Fetal Thymus	thymus
12	chr19:39894800-39896800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:39894800-39896800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr19:39894800-39897000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:39894800-39897200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr19:39894800-39897200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr19:39895000-39895800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:39895000-39895800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr19:39895000-39895800	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr19:39895000-39895800	Enhancers	NHEK	skin
21	chr19:39895000-39896000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:39895000-39896000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:39895000-39896000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:39895000-39896000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr19:39895000-39896000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:39895000-39896000	Weak transcription	Esophagus	oesophagus
27	chr19:39895000-39896000	Weak transcription	Psoas Muscle	Psoas
28	chr19:39895000-39896000	Weak transcription	Right Atrium	heart
29	chr19:39895000-39896000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr19:39895000-39896000	Weak transcription	Thymus	Thymus
31	chr19:39895000-39896000	Enhancers	GM12878-XiMat	blood
32	chr19:39895000-39896000	Weak transcription	K562	blood
33	chr19:39895000-39896200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr19:39895000-39896200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr19:39895000-39896200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:39895000-39896200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:39895000-39896200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:39895000-39896200	Weak transcription	Liver	Liver
39	chr19:39895000-39896200	Enhancers	Colonic Mucosa	Colon
40	chr19:39895000-39896200	Enhancers	Duodenum Mucosa	Duodenum
41	chr19:39895000-39896400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:39895000-39896400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:39895000-39896400	Enhancers	Primary hematopoietic stem cells	blood
44	chr19:39895000-39896400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:39895000-39896400	Enhancers	Fetal Intestine Small	intestine
46	chr19:39895000-39896400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr19:39895000-39896400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr19:39895000-39896600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:39895000-39896600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:39895000-39896600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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