Variant report

Variant	rs28472633
Chromosome Location	chr4:87642390-87642391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87592727..87594779-chr4:87641743..87643865,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10013483	0.89[AFR][1000 genomes]
rs10027356	0.94[AFR][1000 genomes]
rs28404766	0.89[AFR][1000 genomes]
rs28405932	1.00[AFR][1000 genomes]
rs28465411	0.89[AFR][1000 genomes]
rs28470706	0.89[AFR][1000 genomes]
rs28537353	0.84[AFR][1000 genomes]
rs28539152	0.94[AFR][1000 genomes]
rs28568305	1.00[AFR][1000 genomes]
rs28676725	0.83[AFR][1000 genomes]
rs28718854	0.89[AFR][1000 genomes]
rs28725465	0.94[AFR][1000 genomes]
rs28798516	0.89[AFR][1000 genomes]
rs34226837	0.81[AFR][1000 genomes]
rs61160693	1.00[AFR][1000 genomes]
rs72872237	0.97[AFR][1000 genomes]
rs72872254	0.94[AFR][1000 genomes]
rs72872257	0.94[AFR][1000 genomes]
rs72872260	0.94[AFR][1000 genomes]
rs9992507	0.89[AFR][1000 genomes]
rs9994616	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	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
7	nsv508296	chr4:87636350-87667372	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87574600-87644400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:87579200-87642600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:87579400-87644400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:87586400-87643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:87592400-87656400	Weak transcription	Adipose Nuclei	Adipose
6	chr4:87594400-87642600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:87594400-87659800	Weak transcription	Ovary	ovary
8	chr4:87595200-87651200	Weak transcription	Fetal Stomach	stomach
9	chr4:87623400-87643000	Weak transcription	Fetal Lung	lung
10	chr4:87625200-87651600	Weak transcription	Esophagus	oesophagus
11	chr4:87625400-87643400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
13	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
14	chr4:87635400-87648200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:87635600-87651600	Weak transcription	Lung	lung
16	chr4:87636400-87644600	Weak transcription	Fetal Intestine Small	intestine
17	chr4:87636400-87683800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:87636800-87643400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:87637200-87661200	Weak transcription	Pancreas	Pancrea
20	chr4:87638600-87643600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:87638600-87644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:87639000-87643000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:87639200-87688000	Weak transcription	Fetal Intestine Large	intestine
24	chr4:87639400-87739200	Weak transcription	A549	lung
25	chr4:87639600-87643200	Weak transcription	Fetal Kidney	kidney
26	chr4:87639600-87644400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:87639600-87644400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:87639800-87643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:87640200-87643200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:87640200-87652000	Weak transcription	HMEC	breast
31	chr4:87640400-87643000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr4:87640400-87643000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:87640600-87643200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:87641000-87642600	Enhancers	Brain Hippocampus Middle	brain
35	chr4:87641000-87642800	Enhancers	Brain Substantia Nigra	brain
36	chr4:87641200-87642400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:87641200-87642400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:87641200-87642800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr4:87641400-87642400	Enhancers	NHDF-Ad	bronchial
40	chr4:87641400-87642600	Enhancers	Brain Angular Gyrus	brain
41	chr4:87641600-87642400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:87641600-87642600	Enhancers	Brain Cingulate Gyrus	brain
43	chr4:87641600-87642600	Enhancers	Osteobl	bone
44	chr4:87641600-87642800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:87641600-87642800	Enhancers	HUVEC	blood vessel
46	chr4:87641600-87643000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:87641600-87643400	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:87641600-87660400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:87641800-87642400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:87641800-87642400	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links