Variant report

Variant	rs28472461
Chromosome Location	chr4:106956065-106956066
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	chr4:106954975..106957193-chr4:106960681..106963190,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10010622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010712	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10023586	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10026011	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10033060	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11729561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11729801	0.90[AMR][1000 genomes]
rs11736679	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28597815	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28648796	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28663259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28668834	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28783132	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28786397	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28786712	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28823294	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28843476	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28848568	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28852980	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28857517	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28890246	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7679603	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9996386	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522792	chr4:106895964-106982793	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106953600-106956200	Enhancers	NHDF-Ad	bronchial
2	chr4:106953600-106956800	Enhancers	HSMMtube	muscle
3	chr4:106953800-106957000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:106953800-106959600	Enhancers	HepG2	liver
5	chr4:106954000-106956200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:106954000-106956200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:106954200-106956400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:106954400-106956200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:106954400-106959200	Weak transcription	Pancreas	Pancrea
10	chr4:106954800-106959200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:106955000-106969600	Weak transcription	NHLF	lung
12	chr4:106955200-106966600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:106955400-106956200	Flanking Active TSS	Fetal Heart	heart
14	chr4:106955400-106956200	Enhancers	Fetal Stomach	stomach
15	chr4:106955400-106956400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr4:106955600-106956200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr4:106955600-106956400	Enhancers	Fetal Kidney	kidney
18	chr4:106955800-106956200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr4:106955800-106956200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr4:106955800-106956200	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr4:106955800-106956600	Enhancers	Fetal Muscle Leg	muscle
22	chr4:106955800-106956600	Enhancers	Psoas Muscle	Psoas
23	chr4:106956000-106956200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr4:106956000-106960600	Weak transcription	Fetal Lung	lung
25	chr4:106956000-106961400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:106956000-106969800	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links