Variant report

Variant	rs28575961
Chromosome Location	chr15:72828513-72828514
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72667129..72669616-chr15:72825901..72828662,2	MCF-7	breast:
2	chr15:72820906..72824054-chr15:72827920..72830897,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260339	Chromatin interaction
ENSG00000213614	Chromatin interaction
ENSG00000260729	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12324257	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13329347	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2577576	1.00[AMR][1000 genomes]
rs28396210	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28418777	1.00[ASW][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28451211	1.00[AMR][1000 genomes]
rs28451625	1.00[AMR][1000 genomes]
rs28463280	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28483407	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28575504	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28635032	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28667912	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28687667	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74021506	1.00[AMR][1000 genomes]
rs74022835	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74024328	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
2	nsv534037	chr15:72659210-72964029	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv469704	chr15:72669374-72853927	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
4	nsv482685	chr15:72669374-72853927	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
5	nsv1050558	chr15:72739150-72860350	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
6	nsv542427	chr15:72739150-72860350	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
7	nsv569947	chr15:72800853-72878772	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1054626	chr15:72811402-72867502	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv569948	chr15:72811402-72878772	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
10	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
12	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	esv3430383	chr15:72821093-73035167	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72769600-72832200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr15:72775600-72832800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:72792200-72830800	Weak transcription	HSMM	muscle
4	chr15:72793200-72831400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:72794200-72833200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:72794400-72831600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:72796400-72833000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:72796400-72833000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:72796800-72855400	Weak transcription	Esophagus	oesophagus
10	chr15:72797000-72833000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:72798200-72833000	Weak transcription	Gastric	stomach
12	chr15:72805600-72848200	Weak transcription	Fetal Brain Male	brain
13	chr15:72806400-72831600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:72806400-72833000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:72806600-72846800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:72807600-72833000	Weak transcription	Fetal Intestine Large	intestine
17	chr15:72809000-72833000	Weak transcription	Osteobl	bone
18	chr15:72809000-72855400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:72809200-72829400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:72809200-72832800	Weak transcription	Fetal Lung	lung
21	chr15:72809400-72833000	Weak transcription	Adipose Nuclei	Adipose
22	chr15:72809600-72833000	Weak transcription	HSMMtube	muscle
23	chr15:72811400-72833200	Weak transcription	Right Ventricle	heart
24	chr15:72813600-72831400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:72814400-72830800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:72814400-72831800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr15:72814400-72847000	Weak transcription	Ovary	ovary
28	chr15:72814800-72829800	Weak transcription	Brain Substantia Nigra	brain
29	chr15:72814800-72833000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:72814800-72859200	Weak transcription	Brain Angular Gyrus	brain
31	chr15:72815400-72830600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:72815600-72831800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:72815600-72832800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:72815600-72837200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr15:72815600-72838200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:72815800-72833000	Weak transcription	Primary B cells from cord blood	blood
37	chr15:72815800-72837200	Weak transcription	HepG2	liver
38	chr15:72816200-72830400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:72816200-72831000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr15:72816200-72833000	Weak transcription	Fetal Thymus	thymus
41	chr15:72817600-72829000	Weak transcription	NH-A	brain
42	chr15:72817600-72833000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:72818200-72837200	Weak transcription	A549	lung
44	chr15:72818400-72831200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:72819000-72832800	Weak transcription	Fetal Muscle Leg	muscle
46	chr15:72819000-72832800	Weak transcription	Placenta	Placenta
47	chr15:72819600-72837000	Weak transcription	Colon Smooth Muscle	Colon
48	chr15:72819800-72832800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:72819800-72833200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:72820000-72831400	Weak transcription	Monocytes-CD14+_RO01746	blood

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