Variant report

Variant	rs7253804
Chromosome Location	chr19:41231561-41231562
allele	A/C
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	chr19:41231504-41231629	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:41229155-41231687	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41223196..41226143-chr19:41230401..41231962,2	K562	blood:
2	chr19:41220005..41225073-chr19:41230462..41235365,8	K562	blood:
3	chr19:41225203..41228152-chr19:41229042..41232599,3	MCF-7	breast:
4	chr19:41231550..41234206-chr19:41242847..41245259,2	MCF-7	breast:

Variant related genes	Relation type
ITPKC	TF binding region
ENSG00000086544	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11668501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671127	0.94[EUR][1000 genomes]
rs11673492	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12983335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420642	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55993576	1.00[ASN][1000 genomes]
rs66599479	1.00[ASN][1000 genomes]
rs66743282	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66865752	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67083521	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7249805	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7253502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41225200-41235200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41225200-41238800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41225200-41243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:41225600-41231600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr19:41225800-41232000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:41225800-41232200	Weak transcription	Fetal Kidney	kidney
7	chr19:41225800-41233400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:41225800-41233400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:41225800-41236400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:41226400-41246200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:41226600-41238600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr19:41226600-41245600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:41226800-41236600	Weak transcription	GM12878-XiMat	blood
14	chr19:41226800-41245200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:41226800-41245600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:41226800-41245800	Strong transcription	Fetal Stomach	stomach
17	chr19:41227000-41254600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr19:41227200-41232200	Weak transcription	K562	blood
19	chr19:41227200-41237000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:41227200-41255200	Weak transcription	Fetal Heart	heart
21	chr19:41228000-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:41228200-41231800	Strong transcription	Fetal Thymus	thymus
23	chr19:41228200-41238000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr19:41228200-41241400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr19:41228200-41246600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr19:41228200-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:41228400-41234000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:41228600-41232000	Weak transcription	Small Intestine	intestine
29	chr19:41228600-41232200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr19:41228600-41232400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr19:41228600-41233400	Weak transcription	Psoas Muscle	Psoas
32	chr19:41228600-41236000	Weak transcription	Fetal Brain Male	brain
33	chr19:41228600-41236400	Weak transcription	NHDF-Ad	bronchial
34	chr19:41228600-41237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:41228600-41238800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:41228600-41240000	Weak transcription	Stomach Mucosa	stomach
37	chr19:41228600-41240400	Strong transcription	HepG2	liver
38	chr19:41228600-41241200	Strong transcription	A549	lung
39	chr19:41228600-41245400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr19:41228600-41245600	Strong transcription	Fetal Muscle Leg	muscle
41	chr19:41228600-41250000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:41228600-41251000	Strong transcription	Fetal Brain Female	brain
43	chr19:41228800-41234200	Strong transcription	NHEK	skin
44	chr19:41229200-41240800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:41229200-41246800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:41229200-41247200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:41229400-41233800	Strong transcription	Gastric	stomach
48	chr19:41229400-41241200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr19:41229400-41246800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:41229400-41246800	Strong transcription	Monocytes-CD14+_RO01746	blood

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