Variant report

Variant	rs28715047
Chromosome Location	chr1:153550679-153550680
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153547912..153551190-chr1:153580716..153583524,6	MCF-7	breast:
2	chr1:153549778..153551688-chr1:153552692..153554672,3	MCF-7	breast:
3	chr1:153544537..153546118-chr1:153549905..153551639,2	MCF-7	breast:
4	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
5	chr1:153541035..153543212-chr1:153549129..153551158,2	MCF-7	breast:
6	chr1:153548195..153551258-chr1:153612052..153615692,3	MCF-7	breast:
7	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
8	chr1:153548576..153554481-chr1:153583646..153588821,6	MCF-7	breast:
9	chr1:153548336..153551031-chr1:153934523..153936672,2	MCF-7	breast:
10	chr1:153543546..153546056-chr1:153550491..153552553,3	MCF-7	breast:
11	chr1:153549087..153551237-chr1:153598538..153601240,4	MCF-7	breast:
12	chr1:153549624..153551143-chr1:153570106..153572886,2	MCF-7	breast:
13	chr1:153547283..153551329-chr1:153605109..153608605,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271853	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000160679	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs16835464	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28636749	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55815414	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55963294	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60069797	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9660988	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9662163	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662917	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9728377	0.83[ASN][1000 genomes]
rs9729105	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153539600-153554000	Weak transcription	Ovary	ovary
2	chr1:153545800-153551400	Weak transcription	Spleen	Spleen
3	chr1:153546000-153556600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:153546800-153556600	Weak transcription	NH-A	brain
5	chr1:153548800-153552200	Enhancers	Placenta	Placenta
6	chr1:153549400-153551600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:153549400-153551800	Enhancers	HSMMtube	muscle
8	chr1:153549600-153551000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:153549600-153551800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:153549600-153552200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:153549800-153551200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:153549800-153551400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:153549800-153551600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:153549800-153551800	Enhancers	A549	lung
15	chr1:153549800-153551800	Enhancers	NHDF-Ad	bronchial
16	chr1:153549800-153551800	Enhancers	NHLF	lung
17	chr1:153549800-153552000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:153549800-153552000	Enhancers	HSMM	muscle
19	chr1:153549800-153552000	Enhancers	Osteobl	bone
20	chr1:153549800-153552200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:153549800-153552200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:153550200-153551000	Enhancers	Esophagus	oesophagus
23	chr1:153550200-153551200	Enhancers	HMEC	breast
24	chr1:153550200-153551600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:153550200-153551600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr1:153550200-153551800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:153550200-153552000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:153550200-153552000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:153550200-153552000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:153550200-153552000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:153550200-153552200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:153550400-153551000	Weak transcription	Brain Anterior Caudate	brain
33	chr1:153550400-153551200	Enhancers	Adipose Nuclei	Adipose
34	chr1:153550400-153551400	Enhancers	Hela-S3	cervix
35	chr1:153550400-153551600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:153550400-153551600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:153550400-153551800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:153550600-153551000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:153550600-153551800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:153550600-153551800	Enhancers	NHEK	skin
41	chr1:153550600-153552000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:153550600-153556400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:153550600-153560600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links