Variant report

Variant	rs28478343
Chromosome Location	chr15:72476473-72476474
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72471247..72473901-chr15:72474760..72477219,3	MCF-7	breast:
2	chr15:72475748..72478253-chr15:72521364..72524573,3	MCF-7	breast:
3	chr15:72469515..72473441-chr15:72475665..72477509,3	K562	blood:
4	chr15:72476317..72477211-chr15:72493360..72493881,2	MCF-7	breast:
5	chr15:72475452..72478834-chr15:72520641..72523959,4	MCF-7	breast:
6	chr15:72476300..72478148-chr15:72481408..72483163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067225	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10152588	1.00[EUR][1000 genomes]
rs12101457	1.00[AMR][1000 genomes]
rs12101672	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12102191	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12102206	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16956667	1.00[EUR][1000 genomes]
rs2009365	1.00[EUR][1000 genomes]
rs2162236	1.00[EUR][1000 genomes]
rs28368570	1.00[AMR][1000 genomes]
rs28375199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28435418	1.00[EUR][1000 genomes]
rs28446198	1.00[AMR][1000 genomes]
rs28475439	1.00[AMR][1000 genomes]
rs28493313	1.00[AMR][1000 genomes]
rs28526815	1.00[AMR][1000 genomes]
rs28547469	1.00[AMR][1000 genomes]
rs28562796	1.00[EUR][1000 genomes]
rs28564635	1.00[AMR][1000 genomes]
rs28613926	0.87[AMR][1000 genomes]
rs28626831	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28627195	1.00[AMR][1000 genomes]
rs28636457	1.00[AMR][1000 genomes]
rs28663089	1.00[EUR][1000 genomes]
rs28748021	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28758400	1.00[AMR][1000 genomes]
rs28897422	1.00[AMR][1000 genomes]
rs59262103	1.00[EUR][1000 genomes]
rs60790003	1.00[EUR][1000 genomes]
rs61100297	1.00[EUR][1000 genomes]
rs6494999	1.00[EUR][1000 genomes]
rs7175677	1.00[EUR][1000 genomes]
rs7182307	1.00[EUR][1000 genomes]
rs73440566	1.00[EUR][1000 genomes]
rs8039839	1.00[EUR][1000 genomes]
rs8192417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8192427	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:93 , 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	chr15:72476000-72476600	Flanking Active TSS	Hela-S3	cervix
4	chr15:72476000-72476600	Flanking Bivalent TSS/Enh	HepG2	liver
5	chr15:72476000-72476800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:72476000-72476800	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr15:72476000-72477000	Enhancers	Brain Substantia Nigra	brain
8	chr15:72476000-72477000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
9	chr15:72476200-72476600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:72476200-72476600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:72476200-72476600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
12	chr15:72476200-72476600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:72476200-72476600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:72476200-72476600	Enhancers	Aorta	Aorta
15	chr15:72476200-72476600	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr15:72476200-72476600	Bivalent Enhancer	Colon Smooth Muscle	Colon
17	chr15:72476200-72476600	Bivalent Enhancer	Fetal Brain Female	brain
18	chr15:72476200-72476600	Enhancers	Fetal Heart	heart
19	chr15:72476200-72476600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr15:72476200-72476600	Flanking Active TSS	Placenta	Placenta
21	chr15:72476200-72476600	Enhancers	Lung	lung
22	chr15:72476200-72476600	Enhancers	Right Atrium	heart
23	chr15:72476200-72476600	Flanking Active TSS	A549	lung
24	chr15:72476200-72476600	Flanking Active TSS	HSMMtube	muscle
25	chr15:72476200-72476600	Bivalent Enhancer	NH-A	brain
26	chr15:72476200-72476600	Flanking Bivalent TSS/Enh	Osteobl	bone
27	chr15:72476200-72476800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
29	chr15:72476200-72477000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:72476200-72477000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:72476200-72477000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:72476200-72477000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
36	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
37	chr15:72476200-72477000	Bivalent Enhancer	Ovary	ovary
38	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
39	chr15:72476200-72477000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
40	chr15:72476200-72477200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr15:72476200-72477200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr15:72476200-72477200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:72476200-72477200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr15:72476200-72477200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:72476200-72477200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:72476200-72477200	Enhancers	Gastric	stomach
47	chr15:72476200-72477200	Enhancers	Pancreas	Pancrea
48	chr15:72476200-72477200	Enhancers	Placenta Amnion	Placenta Amnion
49	chr15:72476200-72477200	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr15:72476200-72477200	Flanking Active TSS	HSMM	muscle

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