Variant report

Variant	rs28656089
Chromosome Location	chr15:52840542-52840543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52838384..52840575-chr15:52859458..52861427,2	MCF-7	breast:
2	chr15:52838405..52842641-chr15:52848798..52852133,5	MCF-7	breast:
3	chr15:52833192..52836682-chr15:52837514..52841667,6	K562	blood:
4	chr15:52834988..52836682-chr15:52839402..52841667,2	K562	blood:
5	chr15:52839655..52842439-chr15:52848700..52850727,2	MCF-7	breast:
6	chr15:52840038..52842725-chr15:52855232..52857599,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction

Extended variants
information (count: 13 )
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]
rs28711556	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28787300	1.00[AMR][1000 genomes]
rs28863588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73414913	1.00[AMR][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	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
6	esv1001541	chr15:52839342-52843856	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52828800-52850400	Weak transcription	Fetal Brain Male	brain
2	chr15:52830000-52841200	Weak transcription	HepG2	liver
3	chr15:52835800-52845800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:52836200-52851400	Weak transcription	Fetal Kidney	kidney
5	chr15:52836400-52842200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:52836400-52855200	Weak transcription	Small Intestine	intestine
7	chr15:52836600-52844000	Weak transcription	K562	blood
8	chr15:52836600-52844200	Weak transcription	Psoas Muscle	Psoas
9	chr15:52836600-52846000	Weak transcription	Stomach Mucosa	stomach
10	chr15:52836600-52849000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:52836800-52848200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:52837200-52844800	Strong transcription	A549	lung
13	chr15:52837400-52844000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:52837400-52844600	Strong transcription	HSMM	muscle
15	chr15:52837400-52847000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:52837400-52849400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:52837600-52849400	Strong transcription	NHDF-Ad	bronchial
18	chr15:52837600-52852000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:52837800-52840600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:52837800-52841000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:52837800-52842400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr15:52837800-52846000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:52837800-52853000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:52838000-52843400	Strong transcription	Liver	Liver
25	chr15:52838000-52844000	Strong transcription	Adipose Nuclei	Adipose
26	chr15:52838000-52844600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:52838000-52845200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:52838000-52846200	Strong transcription	Primary T cells from cord blood	blood
29	chr15:52838000-52846800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:52838000-52847000	Strong transcription	Fetal Thymus	thymus
31	chr15:52838000-52849200	Strong transcription	Osteobl	bone
32	chr15:52838000-52849400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr15:52838000-52853000	Strong transcription	Dnd41	blood
34	chr15:52838200-52841000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:52838200-52843400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:52838200-52844600	Strong transcription	NHEK	skin
37	chr15:52838200-52844800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr15:52838200-52845800	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr15:52838200-52849000	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:52838200-52849200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:52838200-52849400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:52838200-52850000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:52838400-52842200	Weak transcription	Colon Smooth Muscle	Colon
44	chr15:52838400-52845000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr15:52838400-52846000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:52838400-52846200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr15:52838600-52843200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:52838600-52844600	Strong transcription	Placenta	Placenta
49	chr15:52838600-52845400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:52838600-52846200	Strong transcription	Thymus	Thymus

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