Variant report

Variant	rs16964653
Chromosome Location	chr15:52265415-52265416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:52265280-52265573	HepG2	liver:	n/a	n/a
2	CEBPB	chr15:52265140-52265635	MCF-7	breast:	n/a	n/a
3	CEBPB	chr15:52265123-52265666	MCF-7	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52261233..52265470-chr15:52469433..52474401,7	MCF-7	breast:
2	chr15:52262145..52266701-chr15:52309209..52314377,19	MCF-7	breast:
3	chr15:52262628..52265811-chr15:52469801..52473537,4	MCF-7	breast:
4	chr15:52263208..52265625-chr15:52404085..52407650,4	MCF-7	breast:
5	chr15:52262270..52265607-chr15:52309730..52314612,10	K562	blood:
6	chr15:52244109..52249001-chr15:52262072..52265545,5	MCF-7	breast:
7	chr15:52264141..52265648-chr15:52426026..52428333,2	MCF-7	breast:
8	chr15:52259207..52267788-chr15:52308373..52314434,24	MCF-7	breast:
9	chr15:52262263..52265564-chr15:52309489..52315686,9	K562	blood:
10	chr15:52264304..52267297-chr15:52410135..52412517,2	MCF-7	breast:

No data

Variant related genes	Relation type
LEO1	TF binding region
ENSG00000166477	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000137875	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16953079	0.90[AFR][1000 genomes]
rs16964517	0.85[AFR][1000 genomes]
rs16964530	0.90[AFR][1000 genomes]
rs16964531	0.85[AFR][1000 genomes]
rs4545757	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58356723	0.90[AFR][1000 genomes]
rs58958163	0.90[AFR][1000 genomes]
rs59522140	0.90[AFR][1000 genomes]
rs73396618	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73407384	0.90[AFR][1000 genomes]
rs73407388	0.90[AFR][1000 genomes]
rs73407392	0.90[AFR][1000 genomes]
rs73407393	0.90[AFR][1000 genomes]
rs73409029	0.90[AFR][1000 genomes]
rs73409034	0.90[AFR][1000 genomes]
rs73409044	0.90[AFR][1000 genomes]
rs73409087	0.95[AFR][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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv569410	chr15:52257874-52273132	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv15501	chr15:52265256-52273371	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52264600-52265600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:52264600-52265600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr15:52264600-52265800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:52264600-52266000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:52264600-52266000	Enhancers	Placenta	Placenta
6	chr15:52264600-52266400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:52264600-52273000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr15:52264600-52273000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:52264600-52273000	Weak transcription	Liver	Liver
10	chr15:52264600-52273000	Weak transcription	Right Ventricle	heart
11	chr15:52264600-52273600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:52264600-52273600	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:52264600-52273600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:52264600-52273600	Weak transcription	Stomach Mucosa	stomach
15	chr15:52264600-52273800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:52264600-52273800	Weak transcription	Brain Anterior Caudate	brain
17	chr15:52264600-52273800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:52264600-52273800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:52264600-52273800	Weak transcription	Brain Substantia Nigra	brain
20	chr15:52264600-52273800	Weak transcription	Thymus	Thymus
21	chr15:52264600-52274000	Weak transcription	Colonic Mucosa	Colon
22	chr15:52264600-52274200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr15:52264600-52274400	Weak transcription	Pancreas	Pancrea
24	chr15:52264800-52265600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:52264800-52265600	Enhancers	Dnd41	blood
26	chr15:52264800-52266600	Weak transcription	Brain Germinal Matrix	brain
27	chr15:52264800-52269600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:52264800-52273000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:52264800-52273000	Weak transcription	Hela-S3	cervix
30	chr15:52264800-52273200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:52264800-52273200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:52264800-52273600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:52264800-52273600	Weak transcription	NHEK	skin
34	chr15:52264800-52273800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr15:52264800-52273800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:52264800-52273800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:52264800-52273800	Weak transcription	Fetal Muscle Leg	muscle
38	chr15:52264800-52274000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr15:52264800-52274000	Weak transcription	Fetal Intestine Large	intestine
40	chr15:52265000-52266000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr15:52265000-52267200	Weak transcription	Fetal Stomach	stomach
42	chr15:52265000-52273000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:52265000-52273800	Weak transcription	HSMM	muscle
44	chr15:52265200-52265800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr15:52265200-52265800	Weak transcription	Fetal Intestine Small	intestine
46	chr15:52265200-52266600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:52265200-52267200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:52265200-52269800	Weak transcription	Fetal Brain Female	brain
49	chr15:52265200-52273000	Weak transcription	Fetal Thymus	thymus
50	chr15:52265200-52273800	Weak transcription	Primary T cells fromperipheralblood	blood

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