Variant report

Variant	rs28709904
Chromosome Location	chr15:79280235-79280236
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:79280149-79281427	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:79280068-79281185	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:79280076-79281261	HepG2	liver:	n/a	n/a
4	MAX	chr15:79280097-79280247	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:79280225-79280650	HepG2	liver:	n/a	n/a
6	RUNX3	chr15:79279935-79280265	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:79223166..79226414-chr15:79279938..79282218,3	MCF-7	breast:
2	chr15:79278181..79281070-chr15:79299396..79302014,2	K562	blood:
3	chr15:79267805..79270419-chr15:79279866..79282392,3	MCF-7	breast:
4	chr15:79270685..79272410-chr15:79279786..79282271,2	MCF-7	breast:

No data

Variant related genes	Relation type
RASGRF1	TF binding region
ENSG00000058335	Chromatin interaction
ENSG00000103811	Chromatin interaction
ENSG00000177699	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12101364	1.00[EUR][1000 genomes]
rs16970387	0.81[EUR][1000 genomes]
rs28368520	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28391216	1.00[EUR][1000 genomes]
rs28407629	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28427472	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28461937	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464364	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501391	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501618	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28513164	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28516885	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28546944	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28547879	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28549817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28557276	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28565526	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28567804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28587174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28603308	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28624404	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651192	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28674868	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28683537	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705105	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28716558	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28718997	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28722773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28738778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920807	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904433	chr15:79243571-79310288	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79244000-79288000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:79261200-79280400	Weak transcription	Esophagus	oesophagus
3	chr15:79272200-79280400	Weak transcription	Brain Substantia Nigra	brain
4	chr15:79272200-79280600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:79272200-79284400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:79272400-79286400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr15:79276200-79280400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:79276200-79280600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:79276200-79280600	Weak transcription	Lung	lung
10	chr15:79276400-79280400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr15:79276400-79288600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:79276400-79309200	Weak transcription	Right Atrium	heart
13	chr15:79277400-79280400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr15:79277400-79282000	Weak transcription	Brain Angular Gyrus	brain
15	chr15:79277600-79284000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:79278400-79290400	Enhancers	Fetal Intestine Small	intestine
17	chr15:79279000-79280600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:79279400-79287000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:79279600-79281800	Enhancers	GM12878-XiMat	blood
20	chr15:79279600-79291000	Enhancers	Fetal Intestine Large	intestine
21	chr15:79279800-79282600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:79279800-79285600	Enhancers	HepG2	liver
23	chr15:79280000-79281200	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr15:79280000-79282000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:79280000-79282400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:79280000-79282400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr15:79280000-79282400	Enhancers	HMEC	breast
28	chr15:79280000-79282400	Enhancers	NHDF-Ad	bronchial
29	chr15:79280000-79282400	Enhancers	NHEK	skin
30	chr15:79280000-79283000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:79280000-79283800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr15:79280000-79286800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:79280200-79280400	Enhancers	Brain Cingulate Gyrus	brain
34	chr15:79280200-79280400	Enhancers	Small Intestine	intestine
35	chr15:79280200-79280600	Enhancers	Brain Hippocampus Middle	brain
36	chr15:79280200-79280600	Enhancers	Duodenum Mucosa	Duodenum
37	chr15:79280200-79280800	Enhancers	Brain Anterior Caudate	brain
38	chr15:79280200-79280800	Enhancers	Pancreas	Pancrea
39	chr15:79280200-79281200	Enhancers	Gastric	stomach
40	chr15:79280200-79281600	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr15:79280200-79281600	Enhancers	HUVEC	blood vessel
42	chr15:79280200-79282000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:79280200-79282400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:79280200-79282600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr15:79280200-79282800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr15:79280200-79282800	Enhancers	Adipose Nuclei	Adipose
47	chr15:79280200-79283200	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr15:79280200-79285000	Enhancers	HSMM	muscle
49	chr15:79280200-79286000	Enhancers	HSMMtube	muscle
50	chr15:79280200-79286400	Enhancers	Placenta	Placenta

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