Variant report

Variant	rs2306793
Chromosome Location	chr15:52350879-52350880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52309859..52315433-chr15:52338782..52357079,28	MCF-7	breast:
2	chr15:52348651..52350159-chr15:52350189..52352122,2	K562	blood:
3	chr15:52310181..52316125-chr15:52344513..52354209,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10152141	1.00[EUR][1000 genomes]
rs10518675	1.00[EUR][1000 genomes]
rs12324384	0.83[EUR][1000 genomes]
rs12324807	0.83[EUR][1000 genomes]
rs13379854	0.83[EUR][1000 genomes]
rs16964720	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17540338	0.81[AMR][1000 genomes]
rs2001741	1.00[EUR][1000 genomes]
rs2017967	0.83[EUR][1000 genomes]
rs2899484	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3099571	0.86[EUR][1000 genomes]
rs4774606	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775995	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775996	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55705935	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55873482	1.00[EUR][1000 genomes]
rs56307802	1.00[EUR][1000 genomes]
rs58000475	0.86[EUR][1000 genomes]
rs58936667	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61546369	0.86[EUR][1000 genomes]
rs7177328	1.00[EUR][1000 genomes]
rs7359204	1.00[EUR][1000 genomes]
rs74013636	1.00[EUR][1000 genomes]
rs74013638	1.00[EUR][1000 genomes]
rs74013640	1.00[EUR][1000 genomes]
rs74013641	1.00[EUR][1000 genomes]
rs74013642	1.00[EUR][1000 genomes]
rs74013644	1.00[EUR][1000 genomes]
rs74013645	1.00[EUR][1000 genomes]
rs74013646	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74013647	1.00[EUR][1000 genomes]
rs74013648	1.00[EUR][1000 genomes]
rs74013654	1.00[EUR][1000 genomes]
rs74013656	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74013657	0.81[AMR][1000 genomes]
rs74013659	0.81[AMR][1000 genomes]
rs74013661	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7497554	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8027276	0.83[EUR][1000 genomes]
rs8033365	1.00[EUR][1000 genomes]
rs8036048	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 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	chr15:52314400-52359800	Weak transcription	Fetal Brain Male	brain
2	chr15:52332600-52361800	Weak transcription	Gastric	stomach
3	chr15:52333000-52351000	Weak transcription	Spleen	Spleen
4	chr15:52334000-52361400	Weak transcription	Small Intestine	intestine
5	chr15:52334600-52357200	Weak transcription	Fetal Heart	heart
6	chr15:52337600-52360600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:52337800-52357000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:52338200-52351000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr15:52339200-52351000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr15:52339200-52351200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:52339200-52351600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:52339400-52359200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:52339600-52357000	Strong transcription	Fetal Intestine Large	intestine
14	chr15:52340200-52362200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:52341600-52357600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:52341800-52358000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:52343000-52359400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:52343200-52352000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:52343200-52352000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:52344200-52356600	Strong transcription	Primary T cells from cord blood	blood
21	chr15:52344400-52357200	Strong transcription	Left Ventricle	heart
22	chr15:52344600-52362000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr15:52345000-52351000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:52345000-52357200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:52345000-52357800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:52345000-52358600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:52345200-52358000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr15:52345600-52351000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:52345600-52351000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:52345600-52352600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:52345600-52358000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:52345600-52358800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:52345600-52358800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:52345800-52359200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:52346200-52359000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:52346400-52357200	Strong transcription	NHEK	skin
37	chr15:52347000-52357600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:52347200-52353200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr15:52347200-52356200	Strong transcription	Fetal Lung	lung
40	chr15:52347200-52356600	Strong transcription	Placenta	Placenta
41	chr15:52347200-52357000	Strong transcription	Fetal Thymus	thymus
42	chr15:52347200-52357200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr15:52347200-52358800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:52347400-52357400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:52347600-52354400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:52347600-52356000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:52347600-52356400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:52347600-52356400	Strong transcription	HepG2	liver
49	chr15:52347600-52358800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:52347800-52351000	Weak transcription	Brain Angular Gyrus	brain

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