Variant report

Variant	rs28393460
Chromosome Location	chr15:72476922-72476923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:72476582..72478189-chr7:104650247..104653086,2	MCF-7	breast:
2	chr15:72476500..72479008-chr15:72515049..72516702,2	MCF-7	breast:
3	chr15:72471247..72473901-chr15:72474760..72477219,3	MCF-7	breast:
4	chr15:72475748..72478253-chr15:72521364..72524573,3	MCF-7	breast:
5	chr15:72469515..72473441-chr15:72475665..72477509,3	K562	blood:
6	chr15:72476317..72477211-chr15:72493360..72493881,2	MCF-7	breast:
7	chr15:72475452..72478834-chr15:72520641..72523959,4	MCF-7	breast:
8	chr15:72476533..72478146-chr15:72764010..72766539,2	MCF-7	breast:
9	chr15:72476300..72478148-chr15:72481408..72483163,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000067225	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs13329116	1.00[AMR][1000 genomes]
rs13329270	1.00[AMR][1000 genomes]
rs13329340	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28367264	1.00[AMR][1000 genomes]
rs28373432	1.00[AMR][1000 genomes]
rs28378260	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28379334	1.00[AMR][1000 genomes]
rs28396234	1.00[AMR][1000 genomes]
rs28397237	1.00[AMR][1000 genomes]
rs28403882	1.00[AMR][1000 genomes]
rs28408067	1.00[AMR][1000 genomes]
rs28428645	1.00[AMR][1000 genomes]
rs28429589	1.00[AMR][1000 genomes]
rs28445807	1.00[AMR][1000 genomes]
rs28448787	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28450008	1.00[AMR][1000 genomes]
rs28450424	1.00[AMR][1000 genomes]
rs28451732	1.00[AMR][1000 genomes]
rs28455090	1.00[AMR][1000 genomes]
rs28456991	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28470660	1.00[AMR][1000 genomes]
rs28482979	1.00[AMR][1000 genomes]
rs28483934	1.00[AMR][1000 genomes]
rs28504509	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28514321	1.00[AMR][1000 genomes]
rs28529658	1.00[AMR][1000 genomes]
rs28536592	1.00[AMR][1000 genomes]
rs28542557	1.00[AMR][1000 genomes]
rs28543029	1.00[AMR][1000 genomes]
rs28547979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28548453	1.00[AMR][1000 genomes]
rs28552371	1.00[AMR][1000 genomes]
rs28553452	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28569017	1.00[AMR][1000 genomes]
rs28570214	1.00[AMR][1000 genomes]
rs28573725	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28583168	1.00[AMR][1000 genomes]
rs28589979	1.00[AMR][1000 genomes]
rs28605814	1.00[AMR][1000 genomes]
rs28628140	1.00[AMR][1000 genomes]
rs28628792	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28634283	1.00[AMR][1000 genomes]
rs28636054	1.00[AMR][1000 genomes]
rs28639590	1.00[AMR][1000 genomes]
rs28642081	1.00[AMR][1000 genomes]
rs28643436	1.00[AMR][1000 genomes]
rs28643497	1.00[AMR][1000 genomes]
rs28654176	1.00[AMR][1000 genomes]
rs28654851	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28654861	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28657431	1.00[AMR][1000 genomes]
rs28658414	1.00[AMR][1000 genomes]
rs28660217	1.00[AMR][1000 genomes]
rs28660581	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28663692	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28667521	1.00[AMR][1000 genomes]
rs28675378	1.00[AMR][1000 genomes]
rs28701136	1.00[AMR][1000 genomes]
rs28707151	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28707565	1.00[AMR][1000 genomes]
rs28725348	1.00[AMR][1000 genomes]
rs28727443	1.00[AMR][1000 genomes]
rs28741048	1.00[AMR][1000 genomes]
rs28786091	1.00[AMR][1000 genomes]
rs28791192	1.00[AMR][1000 genomes]
rs28801155	1.00[AMR][1000 genomes]
rs28808678	1.00[AMR][1000 genomes]
rs28824293	1.00[AMR][1000 genomes]
rs28830268	1.00[AMR][1000 genomes]
rs28833566	1.00[AMR][1000 genomes]
rs28853032	1.00[AMR][1000 genomes]
rs28872877	1.00[AMR][1000 genomes]
rs28879707	1.00[AMR][1000 genomes]
rs8192372	1.00[AMR][1000 genomes]
rs9920204	1.00[AMR][1000 genomes]
rs9920223	1.00[AMR][1000 genomes]
rs9920987	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	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72475000-72477200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:72475200-72477000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:72476000-72477000	Enhancers	Brain Substantia Nigra	brain
4	chr15:72476000-72477000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
5	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
6	chr15:72476200-72477000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:72476200-72477000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:72476200-72477000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:72476200-72477000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
13	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
14	chr15:72476200-72477000	Bivalent Enhancer	Ovary	ovary
15	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
16	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
17	chr15:72476200-72477200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr15:72476200-72477200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr15:72476200-72477200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:72476200-72477200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr15:72476200-72477200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:72476200-72477200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:72476200-72477200	Enhancers	Gastric	stomach
24	chr15:72476200-72477200	Enhancers	Pancreas	Pancrea
25	chr15:72476200-72477200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr15:72476200-72477200	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr15:72476200-72477200	Flanking Active TSS	HSMM	muscle
28	chr15:72476200-72477200	Flanking Active TSS	NHEK	skin
29	chr15:72476200-72477400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
30	chr15:72476400-72477000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
31	chr15:72476400-72477000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:72476400-72477000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:72476400-72477000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
34	chr15:72476400-72477000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:72476400-72477000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
36	chr15:72476400-72477000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:72476400-72477000	Enhancers	Liver	Liver
38	chr15:72476400-72477000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
39	chr15:72476400-72477000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr15:72476400-72477000	Bivalent Enhancer	Fetal Brain Male	brain
41	chr15:72476400-72477000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
42	chr15:72476400-72477000	Flanking Active TSS	Psoas Muscle	Psoas
43	chr15:72476400-72477000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
44	chr15:72476400-72477000	Flanking Active TSS	Right Ventricle	heart
45	chr15:72476400-72477000	Flanking Active TSS	HMEC	breast
46	chr15:72476400-72477200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:72476400-72477200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
48	chr15:72476400-72477200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
49	chr15:72476400-72477400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr15:72476600-72477000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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