Variant report

Variant	rs28733880
Chromosome Location	chr4:78980514-78980515
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78980165..78981369-chr4:79437966..79439156,9	MCF-7	breast:
2	chr4:78980443..78981479-chr4:79437986..79438999,5	MCF-7	breast:
3	chr4:78978883..78980863-chr4:79393127..79395107,2	MCF-7	breast:
4	chr4:78980297..78981139-chr4:79092342..79093264,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10016219	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10016229	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10016432	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1502881	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1502882	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1502883	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1502884	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1502885	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1502886	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2036454	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055493	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28627760	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4591635	0.81[EUR][1000 genomes]
rs4597857	0.82[EUR][1000 genomes]
rs4615194	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859907	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859908	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859909	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859912	0.83[EUR][1000 genomes]
rs7659437	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7689647	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs873453	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs873454	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs873455	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv4396	chr4:78935347-78980705	Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78977000-78980800	Active TSS	Left Ventricle	heart
2	chr4:78977000-78981200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:78977200-78980800	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr4:78977200-78980800	Active TSS	Psoas Muscle	Psoas
5	chr4:78977200-78981000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:78977200-78981000	Active TSS	Brain Angular Gyrus	brain
7	chr4:78977200-78981000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:78977200-78981000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr4:78977200-78981000	Active TSS	Right Ventricle	heart
10	chr4:78977200-78981000	Active TSS	A549	lung
11	chr4:78977200-78981200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:78977200-78981400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr4:78977400-78980800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:78977400-78980800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:78977400-78980800	Active TSS	Aorta	Aorta
16	chr4:78977400-78980800	Active TSS	Fetal Heart	heart
17	chr4:78977400-78980800	Active TSS	Hela-S3	cervix
18	chr4:78977400-78981000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:78977400-78981000	Active TSS	HSMMtube	muscle
20	chr4:78977400-78981600	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr4:78977400-78982000	Active TSS	H1 Cell Line	embryonic stem cell
22	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
23	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
24	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
25	chr4:78977600-78980600	Active TSS	Gastric	stomach
26	chr4:78977600-78980600	Bivalent/Poised TSS	HepG2	liver
27	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
28	chr4:78977600-78980800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:78977600-78980800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
30	chr4:78977600-78981000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:78977600-78981000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:78977600-78981000	Active TSS	Fetal Intestine Large	intestine
33	chr4:78977600-78981000	Active TSS	Fetal Intestine Small	intestine
34	chr4:78977600-78981200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:78977600-78981200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr4:78977600-78981200	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr4:78977600-78981600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:78977600-78981800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:78977800-78980600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
40	chr4:78977800-78980800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
41	chr4:78977800-78980800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
42	chr4:78977800-78980800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:78977800-78980800	Active TSS	Ovary	ovary
44	chr4:78977800-78981000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr4:78977800-78981000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:78977800-78981000	Active TSS	Right Atrium	heart
47	chr4:78978000-78980600	Active TSS	NHEK	skin
48	chr4:78978000-78980800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:78978000-78980800	Active TSS	Fetal Lung	lung
50	chr4:78978000-78980800	Active TSS	NHDF-Ad	bronchial

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