Variant report

Variant	rs579496
Chromosome Location	chr19:56144987-56144988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr19:56144842-56145472	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56135134..56137131-chr19:56144636..56147133,4	MCF-7	breast:
2	chr19:55971044..55973132-chr19:56142310..56146274,4	MCF-7	breast:
3	chr1:110948254..110950984-chr19:56143128..56145485,2	MCF-7	breast:
4	chr19:56143909..56147540-chr19:56180767..56182811,3	MCF-7	breast:
5	chr19:56141613..56145221-chr19:56145237..56148178,3	K562	blood:
6	chr19:55916632..55921194-chr19:56143912..56146949,5	K562	blood:
7	chr19:56137436..56140208-chr19:56143830..56146164,3	MCF-7	breast:
8	chr19:55916987..55920426-chr19:56143247..56147032,3	MCF-7	breast:
9	chr19:55917719..55921194-chr19:56143842..56149725,7	K562	blood:
10	chr19:56123360..56125728-chr19:56143804..56146332,2	K562	blood:
11	chr19:56123203..56125337-chr19:56143118..56145205,2	MCF-7	breast:
12	chr19:56131862..56136924-chr19:56144839..56148352,5	MCF-7	breast:
13	chr19:55997044..55998759-chr19:56143237..56145696,2	K562	blood:

No data

Variant related genes	Relation type
ZNF580	TF binding region
ZNF581	TF binding region
ENSG00000224699	Chromatin interaction
ENSG00000267096	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000134248	Chromatin interaction
ENSG00000090971	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1808393	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864434	0.93[ASN][1000 genomes]
rs485152	0.93[ASN][1000 genomes]
rs504850	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs519856	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs596075	0.95[ASN][1000 genomes]
rs643368	0.93[ASN][1000 genomes]
rs664684	0.82[ASN][1000 genomes]
rs7247677	0.81[ASN][1000 genomes]
rs7252055	0.91[ASN][1000 genomes]
rs889092	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][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	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	67 gene(s)	inside rSNPs	diseases
9	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
10	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
11	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs579496	ZNF580	cis	Artery Tibial	GTEx
rs579496	ZNF580	cis	Adipose Subcutaneous	GTEx
rs579496	ZNF580	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56136400-56145600	Weak transcription	Right Atrium	heart
2	chr19:56136400-56146200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:56136800-56145200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr19:56136800-56145200	Weak transcription	Fetal Muscle Leg	muscle
5	chr19:56136800-56145600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:56137200-56145800	Weak transcription	Fetal Brain Female	brain
7	chr19:56138800-56145600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:56143000-56145400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:56143000-56145600	Enhancers	Primary hematopoietic stem cells	blood
10	chr19:56143000-56145800	Enhancers	K562	blood
11	chr19:56143200-56145400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:56143400-56145600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:56143400-56145800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:56143400-56145800	Weak transcription	Fetal Intestine Large	intestine
15	chr19:56143400-56146400	Weak transcription	Fetal Heart	heart
16	chr19:56143600-56145800	Weak transcription	NHEK	skin
17	chr19:56143800-56145400	Weak transcription	HepG2	liver
18	chr19:56143800-56145600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr19:56143800-56145600	Weak transcription	A549	lung
20	chr19:56143800-56145800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:56143800-56145800	Weak transcription	Colonic Mucosa	Colon
22	chr19:56144000-56145400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:56144000-56145400	Weak transcription	Hela-S3	cervix
24	chr19:56144000-56145800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr19:56144200-56145200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:56144200-56145200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:56144200-56145200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:56144200-56145200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr19:56144200-56145200	Weak transcription	Liver	Liver
30	chr19:56144200-56145200	Weak transcription	Placenta	Placenta
31	chr19:56144200-56145200	Weak transcription	Pancreas	Pancrea
32	chr19:56144200-56145200	Weak transcription	Psoas Muscle	Psoas
33	chr19:56144200-56145200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:56144200-56145200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr19:56144200-56145400	Weak transcription	Primary B cells from cord blood	blood
36	chr19:56144200-56145400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:56144200-56145400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr19:56144200-56145400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:56144200-56145400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr19:56144200-56145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:56144200-56145400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:56144200-56145400	Weak transcription	Adipose Nuclei	Adipose
43	chr19:56144200-56145400	Weak transcription	Brain Angular Gyrus	brain
44	chr19:56144200-56145400	Weak transcription	Brain Substantia Nigra	brain
45	chr19:56144200-56145400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr19:56144200-56145400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr19:56144200-56145400	Weak transcription	Fetal Lung	lung
48	chr19:56144200-56145400	Weak transcription	Fetal Stomach	stomach
49	chr19:56144200-56145400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:56144200-56145400	Weak transcription	GM12878-XiMat	blood

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