Variant report

Variant	rs162828
Chromosome Location	chr19:53078641-53078642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53073322..53075540-chr19:53075629..53079478,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167562	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10460164	0.80[EUR][1000 genomes]
rs10460165	0.81[EUR][1000 genomes]
rs162827	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs162830	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs162832	0.83[ASN][1000 genomes]
rs179320	0.87[EUR][1000 genomes]
rs35676304	0.81[EUR][1000 genomes]
rs366793	0.89[EUR][1000 genomes]
rs373554	0.89[EUR][1000 genomes]
rs587238	0.89[EUR][1000 genomes]
rs59524734	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv912304	chr19:53071155-53114267	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53074200-53079200	Weak transcription	Brain Substantia Nigra	brain
2	chr19:53074200-53079400	Weak transcription	Psoas Muscle	Psoas
3	chr19:53074200-53080000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:53074200-53083600	Weak transcription	NH-A	brain
5	chr19:53074200-53087800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:53074400-53079200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:53074400-53079600	Weak transcription	HUVEC	blood vessel
8	chr19:53074400-53085800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
9	chr19:53074600-53079400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:53074600-53079400	Weak transcription	Brain Germinal Matrix	brain
11	chr19:53074600-53079400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr19:53074600-53079400	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:53074600-53079600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:53074600-53079800	Weak transcription	NHDF-Ad	bronchial
15	chr19:53074600-53084800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:53074600-53085800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:53074600-53087400	Weak transcription	Fetal Heart	heart
18	chr19:53074600-53088000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr19:53074600-53103600	Weak transcription	Fetal Brain Male	brain
20	chr19:53074800-53079400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr19:53074800-53079800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:53075000-53079600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:53075000-53079600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:53075000-53082000	Strong transcription	Fetal Muscle Leg	muscle
25	chr19:53075000-53082600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:53075200-53079600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:53075200-53080600	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr19:53075200-53081600	Weak transcription	Right Ventricle	heart
29	chr19:53075200-53082200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:53075200-53082200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:53075400-53079800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:53075400-53079800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr19:53075400-53079800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:53075400-53081800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:53075400-53084400	Strong transcription	Placenta	Placenta
36	chr19:53075400-53089600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:53075400-53092200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:53075400-53092400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:53075400-53092400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
40	chr19:53075600-53079400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr19:53075600-53080200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:53075600-53083400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr19:53075600-53085600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:53075600-53087000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:53075600-53087800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:53075800-53080400	Strong transcription	Fetal Thymus	thymus
47	chr19:53075800-53081400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:53075800-53082000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:53075800-53082400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr19:53075800-53082400	Strong transcription	Left Ventricle	heart

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