Variant report

Variant	rs56840895
Chromosome Location	chr15:52406490-52406491
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52263208..52265625-chr15:52404085..52407650,4	MCF-7	breast:
2	chr15:52404951..52408390-chr15:52415652..52417848,3	K562	blood:
3	chr15:52403961..52406655-chr15:52470750..52472609,2	MCF-7	breast:
4	chr15:52404464..52407280-chr15:52415315..52418015,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000259709	Chromatin interaction
ENSG00000259577	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2231288	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55783485	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56019577	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56254654	0.91[AFR][1000 genomes]
rs56709149	0.82[AFR][1000 genomes]
rs74015611	0.86[AFR][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	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
2	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
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52402200-52411400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:52404800-52406600	Weak transcription	Brain Anterior Caudate	brain
3	chr15:52404800-52406800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:52404800-52407600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:52404800-52407800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:52404800-52408000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:52404800-52408200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:52404800-52408400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:52404800-52409800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:52404800-52410600	Enhancers	Adipose Nuclei	Adipose
11	chr15:52404800-52416400	Weak transcription	Aorta	Aorta
12	chr15:52404800-52428000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:52405000-52406600	Weak transcription	Brain Angular Gyrus	brain
14	chr15:52405000-52406600	Weak transcription	Brain Substantia Nigra	brain
15	chr15:52405000-52407600	Weak transcription	HUVEC	blood vessel
16	chr15:52405000-52407800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr15:52405000-52407800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr15:52405000-52408000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:52405000-52408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:52405000-52408400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:52405000-52409800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:52405000-52411800	Weak transcription	Ovary	ovary
23	chr15:52405000-52412000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:52405000-52413200	Weak transcription	Primary T cells from cord blood	blood
25	chr15:52405000-52414800	Weak transcription	Primary B cells from cord blood	blood
26	chr15:52405000-52416400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:52405000-52416400	Weak transcription	Gastric	stomach
28	chr15:52405000-52416600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:52405000-52416600	Weak transcription	Esophagus	oesophagus
30	chr15:52405000-52420400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:52405000-52421800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:52405000-52427400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:52405000-52427800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:52405000-52428800	Weak transcription	Fetal Heart	heart
35	chr15:52405200-52406800	Weak transcription	Liver	Liver
36	chr15:52405200-52407600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:52405200-52407800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:52405200-52408200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr15:52405200-52412400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:52405400-52407200	Enhancers	HSMM	muscle
41	chr15:52405400-52426000	Weak transcription	Spleen	Spleen
42	chr15:52405600-52407400	Enhancers	HSMMtube	muscle
43	chr15:52405600-52408000	Enhancers	HepG2	liver
44	chr15:52405600-52412800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:52405800-52407800	Enhancers	Fetal Muscle Leg	muscle
46	chr15:52405800-52408000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:52405800-52408000	Weak transcription	GM12878-XiMat	blood
48	chr15:52406000-52408000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr15:52406000-52410200	Enhancers	Brain Germinal Matrix	brain
50	chr15:52406000-52412400	Weak transcription	Thymus	Thymus

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