Variant report

Variant	rs62122452
Chromosome Location	chr19:56618272-56618273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56617467-56618382	K562	blood:	n/a	n/a
2	POLR2A	chr19:56618140-56618501	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:56618159-56618312	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:56618197-56618298	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:56618269-56618971	HL-60	blood:	n/a	n/a
6	POLR2A	chr19:56618137-56618380	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:56617996-56618996	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:56617935-56618888	A549	lung:	n/a	n/a
9	POLR2A	chr19:56616357-56618960	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr19:56617968-56618729	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:56617729-56618280	K562	blood:	n/a	n/a
12	POLR2A	chr19:56617422-56620971	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56598614..56600130-chr19:56616927..56618591,2	MCF-7	breast:
2	chr19:56615193..56619302-chr19:56653183..56656350,4	MCF-7	breast:
3	chr19:56618269..56620601-chr19:56650918..56652939,2	MCF-7	breast:
4	chr19:56617972..56620643-chr19:56620884..56623590,3	MCF-7	breast:
5	chr19:56617470..56621508-chr19:56630958..56634094,7	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF787	TF binding region
ENSG00000167685	Chromatin interaction
ENSG00000142409	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2279413	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs514916	0.84[EUR][1000 genomes]
rs578901	0.82[EUR][1000 genomes]
rs58893103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59924464	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs606882	0.81[ASN][1000 genomes]
rs62122401	0.82[AMR][1000 genomes]
rs62122402	0.82[AMR][1000 genomes]
rs62122411	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62122445	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62122446	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62122447	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62122448	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62122451	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62122455	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72490744	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv912512	chr19:56592286-56636759	Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
12	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv912514	chr19:56596815-56636759	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
14	nsv912515	chr19:56598829-56623710	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
15	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
16	esv1809307	chr19:56604027-56633623	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	esv1811581	chr19:56609313-56631618	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
18	esv1824038	chr19:56610449-56636632	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56592600-56620000	Weak transcription	HSMMtube	muscle
2	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:56597200-56619400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:56600000-56619000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:56602800-56620000	Weak transcription	NH-A	brain
7	chr19:56603200-56619800	Weak transcription	NHDF-Ad	bronchial
8	chr19:56605200-56619800	Weak transcription	HSMM	muscle
9	chr19:56605200-56620000	Weak transcription	Fetal Kidney	kidney
10	chr19:56608200-56618600	ZNF genes & repeats	Brain Germinal Matrix	brain
11	chr19:56609600-56619600	Weak transcription	Fetal Heart	heart
12	chr19:56613200-56620000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:56613600-56619800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr19:56615000-56619600	Weak transcription	Brain Substantia Nigra	brain
15	chr19:56615000-56620200	Weak transcription	Aorta	Aorta
16	chr19:56616000-56618800	Enhancers	Brain Anterior Caudate	brain
17	chr19:56616000-56618800	Enhancers	Brain Cingulate Gyrus	brain
18	chr19:56616000-56619200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:56616000-56619800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr19:56616000-56626600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr19:56616000-56627000	Enhancers	Liver	Liver
22	chr19:56616000-56627200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr19:56616200-56618800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr19:56616200-56619400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:56616200-56620800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:56616600-56618400	Enhancers	Ovary	ovary
27	chr19:56616600-56618400	Enhancers	HMEC	breast
28	chr19:56616600-56618600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr19:56616600-56620400	Enhancers	Brain Hippocampus Middle	brain
30	chr19:56616800-56618400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr19:56617000-56618600	Genic enhancers	Thymus	Thymus
32	chr19:56617000-56619000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:56617000-56620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr19:56617200-56618600	Strong transcription	Fetal Intestine Large	intestine
35	chr19:56617200-56618800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
36	chr19:56617200-56618800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
37	chr19:56617200-56619000	Weak transcription	Small Intestine	intestine
38	chr19:56617200-56619200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:56617200-56619400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:56617200-56619400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:56617200-56619400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:56617200-56619800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:56617200-56619800	Enhancers	Primary hematopoietic stem cells	blood
44	chr19:56617200-56619800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr19:56617200-56619800	Strong transcription	Fetal Intestine Small	intestine
46	chr19:56617200-56619800	Weak transcription	Fetal Lung	lung
47	chr19:56617200-56620000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:56617200-56620000	Weak transcription	Fetal Brain Female	brain
49	chr19:56617200-56620000	Weak transcription	HUVEC	blood vessel
50	chr19:56617200-56620400	Weak transcription	Primary T cells from cord blood	blood

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