Variant report

Variant	rs28863588
Chromosome Location	chr15:52838546-52838547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52834312..52836237-chr15:52837980..52840201,2	MCF-7	breast:
2	chr15:52838384..52840575-chr15:52859458..52861427,2	MCF-7	breast:
3	chr15:52838405..52842641-chr15:52848798..52852133,5	MCF-7	breast:
4	chr15:52836622..52839186-chr15:52841792..52845841,4	K562	blood:
5	chr15:52833192..52836682-chr15:52837514..52841667,6	K562	blood:
6	chr15:52837831..52839348-chr15:52842783..52844541,2	MCF-7	breast:
7	chr15:52837261..52840412-chr15:52840986..52844425,3	K562	blood:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13329087	1.00[AMR][1000 genomes]
rs28642806	0.81[AFR][1000 genomes]
rs28648824	1.00[AMR][1000 genomes]
rs28656089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28711556	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28787300	1.00[AMR][1000 genomes]
rs73414913	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52822200-52839600	Weak transcription	Right Atrium	heart
2	chr15:52828800-52850400	Weak transcription	Fetal Brain Male	brain
3	chr15:52830000-52841200	Weak transcription	HepG2	liver
4	chr15:52835800-52845800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:52836200-52851400	Weak transcription	Fetal Kidney	kidney
6	chr15:52836400-52842200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:52836400-52855200	Weak transcription	Small Intestine	intestine
8	chr15:52836600-52844000	Weak transcription	K562	blood
9	chr15:52836600-52844200	Weak transcription	Psoas Muscle	Psoas
10	chr15:52836600-52846000	Weak transcription	Stomach Mucosa	stomach
11	chr15:52836600-52849000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:52836800-52848200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:52837000-52838800	Weak transcription	Hela-S3	cervix
14	chr15:52837200-52844800	Strong transcription	A549	lung
15	chr15:52837400-52838800	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr15:52837400-52844000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:52837400-52844600	Strong transcription	HSMM	muscle
18	chr15:52837400-52847000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:52837400-52849400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:52837600-52838600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:52837600-52839000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:52837600-52839000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:52837600-52839200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:52837600-52839200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:52837600-52839200	Strong transcription	Fetal Brain Female	brain
26	chr15:52837600-52849400	Strong transcription	NHDF-Ad	bronchial
27	chr15:52837600-52852000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:52837800-52838600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:52837800-52838600	ZNF genes & repeats	Fetal Intestine Large	intestine
30	chr15:52837800-52838800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:52837800-52839000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr15:52837800-52839000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr15:52837800-52839000	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:52837800-52840000	Strong transcription	Fetal Heart	heart
35	chr15:52837800-52840600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:52837800-52841000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr15:52837800-52842400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr15:52837800-52846000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:52837800-52853000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr15:52838000-52838600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:52838000-52838600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
42	chr15:52838000-52838600	ZNF genes & repeats	Primary B cells from cord blood	blood
43	chr15:52838000-52838600	Enhancers	Primary T cells fromperipheralblood	blood
44	chr15:52838000-52838600	ZNF genes & repeats	Placenta	Placenta
45	chr15:52838000-52838600	ZNF genes & repeats	Thymus	Thymus
46	chr15:52838000-52838800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:52838000-52838800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
48	chr15:52838000-52838800	ZNF genes & repeats	Aorta	Aorta
49	chr15:52838000-52838800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
50	chr15:52838000-52838800	Strong transcription	Fetal Lung	lung

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