Variant report

Variant	rs28657920
Chromosome Location	chr15:55920129-55920130
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	chr15:55818424..55820652-chr15:55918654..55921682,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16976436	0.83[AFR][1000 genomes]
rs28377652	0.89[AFR][1000 genomes]
rs28398229	0.82[AFR][1000 genomes]
rs28399707	0.89[AFR][1000 genomes]
rs28508196	0.89[AFR][1000 genomes]
rs28515086	0.89[AFR][1000 genomes]
rs28523366	0.95[AFR][1000 genomes]
rs28561692	0.95[AFR][1000 genomes]
rs7164393	0.82[AFR][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	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
7	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
8	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv569540	chr15:55866065-55950082	Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55902200-55942200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:55904200-55927000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:55904600-55929400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:55905200-55920200	Weak transcription	HepG2	liver
5	chr15:55906800-55922800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:55908600-55945000	Weak transcription	Left Ventricle	heart
7	chr15:55908800-55938800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:55909800-55920800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:55910000-55920200	Weak transcription	Psoas Muscle	Psoas
10	chr15:55910200-55928600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:55910400-55930800	Weak transcription	Fetal Lung	lung
12	chr15:55910600-55922800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:55910800-55927000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:55911000-55921400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:55911000-55931000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr15:55911800-55977000	Weak transcription	Fetal Intestine Small	intestine
17	chr15:55912200-55920600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:55912200-55929800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:55912400-55944000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:55912600-55920200	Weak transcription	Lung	lung
21	chr15:55915200-55920200	Weak transcription	Fetal Intestine Large	intestine
22	chr15:55916000-55938200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:55916200-55928200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:55917000-55922600	Weak transcription	Fetal Kidney	kidney
25	chr15:55918600-55929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:55918600-55931200	Weak transcription	Ovary	ovary
27	chr15:55919200-55920600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:55919200-55921200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:55919200-55924400	Weak transcription	Aorta	Aorta
30	chr15:55919400-55920400	Enhancers	Placenta	Placenta
31	chr15:55919800-55920400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:55919800-55920600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:55919800-55920600	Enhancers	HUVEC	blood vessel
34	chr15:55919800-55920600	Enhancers	NHEK	skin
35	chr15:55919800-55920800	Enhancers	HMEC	breast
36	chr15:55919800-55921000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:55919800-55921200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:55919800-55924600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:55920000-55920200	Flanking Active TSS	A549	lung
40	chr15:55920000-55920400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr15:55920000-55920400	Flanking Active TSS	Hela-S3	cervix
42	chr15:55920000-55920400	Enhancers	NH-A	brain
43	chr15:55920000-55920400	Flanking Active TSS	Osteobl	bone
44	chr15:55920000-55920600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr15:55920000-55920600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr15:55920000-55920600	Enhancers	HSMM	muscle
47	chr15:55920000-55920600	Flanking Active TSS	NHDF-Ad	bronchial
48	chr15:55920000-55920800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:55920000-55920800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:55920000-55920800	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links