Variant report

Variant	rs62120486
Chromosome Location	chr19:39601539-39601540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:39600198..39604538-chr19:39898809..39902716,7	MCF-7	breast:
2	chr19:39599295..39601915-chr19:39625074..39628012,2	MCF-7	breast:
3	chr19:39542686..39543478-chr19:39600712..39601594,2	MCF-7	breast:
4	chr19:39599349..39603430-chr19:39902751..39905281,3	MCF-7	breast:
5	chr19:39601023..39604135-chr19:39897877..39902850,6	MCF-7	breast:
6	chr11:71157965..71160318-chr19:39600785..39602620,2	MCF-7	breast:
7	chr19:39600818..39603608-chr19:39896434..39898280,2	MCF-7	breast:
8	chr19:39543748..39546255-chr19:39599767..39602313,2	MCF-7	breast:
9	chr19:39520776..39522993-chr19:39601376..39603470,3	MCF-7	breast:
10	chr19:39601113..39601676-chr19:39818467..39819389,3	K562	blood:
11	chr19:39600885..39601696-chr19:39818483..39819058,3	MCF-7	breast:
12	chr19:39600064..39604229-chr19:39615105..39621950,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000172893	Chromatin interaction
ENSG00000269172	Chromatin interaction
ENSG00000254682	Chromatin interaction
ENSG00000130669	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000161243	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000267992	Chromatin interaction
ENSG00000266559	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11882372	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1313617	0.93[EUR][1000 genomes]
rs2569368	0.91[EUR][1000 genomes]
rs2569369	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28606601	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs516004	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563873	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs565812	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62119549	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62120479	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120480	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120481	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120482	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62120483	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120484	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62120485	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62120488	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62120489	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62120490	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs692346	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692438	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs692461	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs692730	0.92[EUR][1000 genomes]
rs7256505	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7256546	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73045449	0.80[EUR][1000 genomes]
rs774913	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs774915	0.92[EUR][1000 genomes]
rs774916	0.92[EUR][1000 genomes]
rs774917	0.92[EUR][1000 genomes]
rs774918	0.92[EUR][1000 genomes]
rs774919	0.92[EUR][1000 genomes]
rs774920	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1067028	chr19:39567228-39622846	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1060469	chr19:39567228-39624790	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39590400-39602800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:39597600-39602600	Weak transcription	Brain Anterior Caudate	brain
3	chr19:39597800-39603000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr19:39600400-39603200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:39600600-39601600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:39600800-39601600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr19:39600800-39601800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:39600800-39602600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:39600800-39602600	Enhancers	A549	lung
10	chr19:39600800-39606800	Enhancers	Placenta	Placenta
11	chr19:39601000-39601600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr19:39601000-39601600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:39601000-39601600	Enhancers	Brain Angular Gyrus	brain
14	chr19:39601000-39601600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr19:39601200-39601600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:39601200-39601600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr19:39601200-39601600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:39601200-39601600	Enhancers	Brain Substantia Nigra	brain
19	chr19:39601200-39601800	Enhancers	Fetal Kidney	kidney
20	chr19:39601200-39602800	Enhancers	NHEK	skin
21	chr19:39601200-39603200	Enhancers	Fetal Intestine Small	intestine
22	chr19:39601200-39603800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr19:39601400-39601800	Weak transcription	HMEC	breast
24	chr19:39601400-39602000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:39601400-39602200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr19:39601400-39602600	Enhancers	Hela-S3	cervix

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