Variant report

Variant	rs55959303
Chromosome Location	chr19:38894720-38894721
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38892832..38895683-chr19:38905614..38908476,2	K562	blood:
2	chr19:38892751..38895518-chr19:38905731..38908056,2	MCF-7	breast:
3	chr19:38864731..38867116-chr19:38892888..38894994,2	MCF-7	breast:
4	chr19:38864536..38866994-chr19:38891927..38895682,4	MCF-7	breast:
5	chr19:38825542..38827860-chr19:38892803..38895034,2	K562	blood:
6	chr19:38893264..38895978-chr19:39340017..39342861,2	MCF-7	breast:
7	chr19:38873942..38878444-chr19:38892255..38895006,5	K562	blood:
8	chr19:38891109..38897587-chr19:38900077..38906045,7	MCF-7	breast:
9	chr19:38892840..38895111-chr19:38906916..38908853,2	MCF-7	breast:
10	chr19:38810024..38812525-chr19:38892478..38895075,3	MCF-7	breast:
11	chr19:38878160..38880019-chr19:38892423..38895031,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171777	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000267090	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000099337	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12608599	0.92[ASN][1000 genomes]
rs12608644	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12608722	0.97[ASN][1000 genomes]
rs12609258	0.87[ASN][1000 genomes]
rs12610650	0.83[AMR][1000 genomes]
rs2074982	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2286474	0.87[ASN][1000 genomes]
rs2302186	0.92[ASN][1000 genomes]
rs2302227	0.90[ASN][1000 genomes]
rs3745954	0.86[ASN][1000 genomes]
rs3745957	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3745958	0.82[ASN][1000 genomes]
rs3745959	0.82[ASN][1000 genomes]
rs3948666	0.92[ASN][1000 genomes]
rs4432370	0.83[ASN][1000 genomes]
rs45485196	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56854837	0.96[ASN][1000 genomes]
rs57146784	0.81[ASN][1000 genomes]
rs58462889	0.83[AMR][1000 genomes]
rs6508790	0.96[ASN][1000 genomes]
rs72480720	0.80[AMR][1000 genomes];0.92[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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38893200-38894800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38893200-38894800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:38893200-38894800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr19:38893200-38894800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:38893200-38894800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:38893200-38894800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:38893200-38894800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:38893200-38894800	Active TSS	Primary T cells from cord blood	blood
9	chr19:38893200-38894800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:38893200-38894800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:38893200-38894800	Active TSS	Muscle Satellite Cultured Cells	--
12	chr19:38893200-38894800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:38893200-38894800	Active TSS	Brain Angular Gyrus	brain
14	chr19:38893200-38894800	Active TSS	Brain Hippocampus Middle	brain
15	chr19:38893200-38894800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:38893200-38894800	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr19:38893200-38894800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr19:38893200-38894800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr19:38893200-38894800	Active TSS	GM12878-XiMat	blood
20	chr19:38893200-38895000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:38893200-38895000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:38893200-38895200	Active TSS	Rectal Smooth Muscle	rectum
23	chr19:38893400-38894800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:38893400-38894800	Active TSS	Brain Anterior Caudate	brain
25	chr19:38893400-38894800	Active TSS	Colonic Mucosa	Colon
26	chr19:38893400-38894800	Active TSS	Fetal Intestine Small	intestine
27	chr19:38893400-38894800	Active TSS	Pancreas	Pancrea
28	chr19:38893400-38894800	Active TSS	Stomach Mucosa	stomach
29	chr19:38893400-38894800	Active TSS	Thymus	Thymus
30	chr19:38893400-38894800	Active TSS	K562	blood
31	chr19:38893400-38895000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:38893400-38895000	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr19:38893400-38895000	Active TSS	Duodenum Mucosa	Duodenum
34	chr19:38893400-38895000	Active TSS	Fetal Brain Female	brain
35	chr19:38893400-38895000	Active TSS	Osteobl	bone
36	chr19:38893800-38894800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:38894000-38894800	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr19:38894000-38894800	Weak transcription	Fetal Heart	heart
39	chr19:38894200-38894800	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr19:38894200-38895000	Flanking Active TSS	Dnd41	blood
41	chr19:38894200-38895200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr19:38894400-38894800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr19:38894400-38894800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr19:38894400-38894800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:38894400-38894800	Flanking Active TSS	Fetal Stomach	stomach
46	chr19:38894400-38895000	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr19:38894400-38895000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr19:38894400-38895200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:38894400-38895200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:38894400-38895600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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