Variant report

Variant	rs4801720
Chromosome Location	chr19:56912912-56912913
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56902006..56908060-chr19:56909612..56917978,15	K562	blood:
2	chr19:56910743..56913203-chr19:56914097..56915659,2	K562	blood:

Variant related genes	Relation type
ENSG00000198440	Chromatin interaction
ENSG00000266631	Chromatin interaction
ENSG00000267454	Chromatin interaction
ENSG00000018869	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11084447	0.83[ASN][1000 genomes]
rs11084448	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs12709959	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12979827	0.82[ASN][1000 genomes]
rs12984960	0.91[ASN][1000 genomes]
rs2215410	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs2288860	0.82[JPT][hapmap]
rs2288862	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2288863	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28815239	0.85[ASN][1000 genomes]
rs4239475	0.85[ASN][1000 genomes]
rs4801159	0.91[ASN][1000 genomes]
rs4801160	0.91[ASN][1000 genomes]
rs4801161	0.91[ASN][1000 genomes]
rs4801316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801318	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs62121591	0.88[ASN][1000 genomes]
rs62121592	0.85[ASN][1000 genomes]
rs62121594	0.85[ASN][1000 genomes]
rs6509995	1.00[ASN][1000 genomes]
rs7253851	0.91[ASN][1000 genomes]
rs8113270	0.85[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv544096	chr19:56905651-56933455	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4801720	ZNF582-AS1	cis	Esophagus Muscularis	GTEx
rs4801720	ZNF582-AS1	cis	Artery Tibial	GTEx
rs4801720	ZSCAN18	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56905000-56913600	ZNF genes & repeats	Liver	Liver
2	chr19:56905600-56914600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:56905800-56914400	Weak transcription	Fetal Heart	heart
4	chr19:56908000-56913600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:56908000-56913600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:56908000-56914800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:56908200-56913000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
8	chr19:56908200-56914600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:56908400-56913600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:56908600-56913400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr19:56908800-56913600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
12	chr19:56908800-56913600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
13	chr19:56909000-56913600	ZNF genes & repeats	Primary B cells from cord blood	blood
14	chr19:56909200-56913400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
15	chr19:56909400-56913600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
16	chr19:56910000-56914200	ZNF genes & repeats	Dnd41	blood
17	chr19:56910200-56914000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr19:56910400-56913400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:56910400-56914600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
20	chr19:56910600-56914200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:56910600-56914200	Weak transcription	Brain Anterior Caudate	brain
22	chr19:56910600-56914400	Weak transcription	Brain Substantia Nigra	brain
23	chr19:56910600-56914400	Weak transcription	Fetal Brain Male	brain
24	chr19:56910800-56914400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr19:56910800-56914600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:56911000-56914200	Weak transcription	Brain Angular Gyrus	brain
27	chr19:56911000-56914400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:56911000-56914400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:56911000-56914600	Weak transcription	Ovary	ovary
30	chr19:56911000-56914600	Weak transcription	Right Ventricle	heart
31	chr19:56911000-56914800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr19:56911000-56915000	Weak transcription	Aorta	Aorta
33	chr19:56911200-56913000	Weak transcription	HSMMtube	muscle
34	chr19:56911200-56914400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:56911400-56914200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:56912000-56914200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:56912000-56914200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:56912000-56914400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:56912000-56914400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:56912000-56914400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr19:56912000-56914400	Weak transcription	Brain Germinal Matrix	brain
42	chr19:56912000-56914400	Weak transcription	Brain Hippocampus Middle	brain
43	chr19:56912000-56914400	Weak transcription	Fetal Lung	lung
44	chr19:56912200-56914400	Weak transcription	Fetal Kidney	kidney
45	chr19:56912200-56914400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:56912200-56914600	Weak transcription	Left Ventricle	heart
47	chr19:56912400-56914000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:56912800-56913400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
49	chr19:56912800-56913400	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
50	chr19:56912800-56913400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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