Variant report

Variant	rs28899172
Chromosome Location	chr2:234609681-234609682
allele	A/C
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234394239..234398905-chr2:234606921..234610330,8	MCF-7	breast:
2	chr2:234609669..234612575-chr2:234763308..234766192,2	MCF-7	breast:
3	chr2:234474851..234476987-chr2:234608210..234610315,2	MCF-7	breast:
4	chr2:234464274..234466431-chr2:234607467..234610619,3	MCF-7	breast:
5	chr2:234607784..234610773-chr2:234739083..234742311,4	MCF-7	breast:
6	chr2:234606620..234610585-chr2:234612683..234620351,17	MCF-7	breast:
7	chr2:234604730..234606945-chr2:234609647..234612272,2	K562	blood:
8	chr2:234606390..234610516-chr2:234613313..234618925,12	MCF-7	breast:
9	chr2:234393470..234398510-chr2:234607909..234611299,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224814	Chromatin interaction
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28505045	1.00[AMR][1000 genomes]
rs28898569	1.00[AMR][1000 genomes]
rs28898572	1.00[AMR][1000 genomes]
rs28898586	1.00[AMR][1000 genomes]
rs28898588	1.00[AMR][1000 genomes]
rs28898592	1.00[AMR][1000 genomes]
rs28898597	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28898607	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28898610	1.00[AMR][1000 genomes]
rs28899169	1.00[AMR][1000 genomes]
rs28899180	1.00[AMR][1000 genomes]
rs28899184	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28899185	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28969714	1.00[AMR][1000 genomes]
rs28970013	1.00[AMR][1000 genomes]
rs45497792	1.00[AMR][1000 genomes]
rs45594938	1.00[AMR][1000 genomes]
rs45617840	1.00[AMR][1000 genomes]
rs45618133	1.00[AMR][1000 genomes]
rs6735370	1.00[AMR][1000 genomes]
rs6746419	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234602800-234614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:234609000-234610000	Weak transcription	Pancreas	Pancrea
3	chr2:234609000-234610800	Weak transcription	A549	lung
4	chr2:234609000-234611000	Weak transcription	Liver	Liver
5	chr2:234609000-234611000	Weak transcription	HUVEC	blood vessel
6	chr2:234609000-234614400	Weak transcription	Stomach Mucosa	stomach
7	chr2:234609000-234614800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:234609200-234610600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:234609200-234610800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:234609200-234610800	Weak transcription	Hela-S3	cervix
11	chr2:234609200-234611400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:234609200-234614000	Weak transcription	NHEK	skin
13	chr2:234609200-234614200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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