Variant report

Variant	rs28725465
Chromosome Location	chr4:87668677-87668678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87657826..87659557-chr4:87666648..87668755,2	K562	blood:
2	chr4:87666468..87669135-chr4:87669652..87672060,2	MCF-7	breast:
3	chr4:87668227..87671028-chr4:87672154..87674111,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10013483	0.84[AFR][1000 genomes]
rs10027356	0.88[AFR][1000 genomes]
rs28404766	0.84[AFR][1000 genomes]
rs28405932	0.94[AFR][1000 genomes]
rs28465411	0.84[AFR][1000 genomes]
rs28470706	0.84[AFR][1000 genomes]
rs28472633	0.94[AFR][1000 genomes]
rs28539152	1.00[AFR][1000 genomes]
rs28568305	0.94[AFR][1000 genomes]
rs28718854	0.84[AFR][1000 genomes]
rs28798516	0.84[AFR][1000 genomes]
rs61160693	0.94[AFR][1000 genomes]
rs72872237	0.97[AFR][1000 genomes]
rs72872254	1.00[AFR][1000 genomes]
rs72872257	1.00[AFR][1000 genomes]
rs72872260	1.00[AFR][1000 genomes]
rs9992507	0.84[AFR][1000 genomes]
rs9994616	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription 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	6 gene(s)	inside rSNPs	diseases
3	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
2	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
3	chr4:87636400-87683800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:87639200-87688000	Weak transcription	Fetal Intestine Large	intestine
5	chr4:87639400-87739200	Weak transcription	A549	lung
6	chr4:87641800-87683400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:87642200-87692600	Weak transcription	NH-A	brain
8	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:87642600-87692400	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:87642600-87697600	Weak transcription	Brain Angular Gyrus	brain
11	chr4:87642600-87719200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:87644600-87680600	Weak transcription	NHLF	lung
13	chr4:87650400-87677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:87651800-87676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:87652600-87670000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:87655600-87704400	Weak transcription	Hela-S3	cervix
17	chr4:87659000-87676400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:87661600-87671600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:87661600-87671600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:87661600-87680400	Weak transcription	Brain Substantia Nigra	brain
21	chr4:87661600-87680600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:87661600-87683200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:87661600-87710200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:87661600-87711400	Weak transcription	Brain Germinal Matrix	brain
25	chr4:87661600-87712000	Weak transcription	Esophagus	oesophagus
26	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:87661800-87670400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:87661800-87671400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:87661800-87671600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:87661800-87671600	Weak transcription	Lung	lung
31	chr4:87661800-87676600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:87661800-87683000	Weak transcription	Fetal Stomach	stomach
33	chr4:87661800-87683200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:87661800-87683800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:87661800-87708000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:87661800-87712000	Weak transcription	Fetal Intestine Small	intestine
37	chr4:87661800-87728800	Weak transcription	Pancreas	Pancrea
38	chr4:87662000-87669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:87662000-87669200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:87662000-87675600	Weak transcription	Gastric	stomach
41	chr4:87662400-87669600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:87663000-87672200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr4:87663000-87683600	Weak transcription	Fetal Brain Female	brain
44	chr4:87663000-87711400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:87663400-87675400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:87664000-87670800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:87665000-87692400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:87665600-87669800	Strong transcription	Fetal Lung	lung
49	chr4:87665600-87673400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:87665800-87676000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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