Variant report

Variant	rs2244428
Chromosome Location	chr19:52872483-52872484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52771473..52773658-chr19:52872286..52874915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs162116	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162118	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs184922	0.85[EUR][1000 genomes]
rs2244427	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707312	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs707313	0.84[ASN][1000 genomes]
rs780732	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats 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 miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS 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	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52865200-52875400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:52866600-52875400	ZNF genes & repeats	Liver	Liver
3	chr19:52869800-52872600	Weak transcription	Fetal Kidney	kidney
4	chr19:52869800-52872800	Weak transcription	Gastric	stomach
5	chr19:52870000-52872800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:52870000-52872800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:52870000-52872800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:52870000-52872800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:52870000-52872800	Weak transcription	Aorta	Aorta
10	chr19:52870000-52872800	Weak transcription	Fetal Brain Male	brain
11	chr19:52870000-52872800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr19:52870200-52872800	Weak transcription	Brain Angular Gyrus	brain
13	chr19:52870200-52872800	Weak transcription	Brain Anterior Caudate	brain
14	chr19:52870200-52872800	Weak transcription	Brain Substantia Nigra	brain
15	chr19:52870200-52872800	Weak transcription	Ovary	ovary
16	chr19:52871000-52872600	Weak transcription	Brain Germinal Matrix	brain
17	chr19:52871000-52872600	Weak transcription	Fetal Brain Female	brain
18	chr19:52871000-52872800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:52871000-52872800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr19:52871000-52872800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr19:52871000-52872800	Weak transcription	Colon Smooth Muscle	Colon
22	chr19:52871200-52872800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:52871200-52872800	Weak transcription	Brain Hippocampus Middle	brain
24	chr19:52871200-52876400	Weak transcription	Dnd41	blood
25	chr19:52871800-52872600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:52872000-52872800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:52872200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:52872200-52872800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:52872200-52872800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:52872200-52872800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:52872200-52872800	Weak transcription	Fetal Lung	lung
32	chr19:52872200-52872800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:52872400-52872600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:52872400-52872800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr19:52872400-52873600	Active TSS	Monocytes-CD14+_RO01746	blood
36	chr19:52872400-52874000	Active TSS	Duodenum Smooth Muscle	Duodenum

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