Variant report

Variant	rs11562977
Chromosome Location	chr2:234826056-234826057
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	chr2:234761504..234764477-chr2:234824983..234827662,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123485	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10490009	1.00[GIH][hapmap]
rs11562956	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11563068	0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs11563214	0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs11563218	0.82[ASW][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12617866	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs12620352	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs1468521	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16849914	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2362291	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28900703	0.81[AMR][1000 genomes]
rs28900710	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs28900712	0.91[AMR][1000 genomes]
rs28900713	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28901579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28901582	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28901591	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28901600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28901608	0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28901610	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs28901615	1.00[EUR][1000 genomes]
rs28901618	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs28901629	0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes]
rs28901630	0.85[YRI][hapmap]
rs28901637	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs28901868	0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs28902174	0.83[EUR][1000 genomes]
rs3771334	0.91[AMR][1000 genomes]
rs3806588	0.81[AMR][1000 genomes]
rs4663342	0.93[CHB][hapmap];1.00[EUR][1000 genomes]
rs4663343	0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs4663989	0.82[ASW][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs7602303	0.93[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs9789366	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9789398	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9789675	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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
2	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:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234825000-234827200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234825800-234826200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:234825800-234826200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr2:234825800-234826200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr2:234825800-234826400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr2:234825800-234826600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr2:234825800-234826600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:234826000-234826200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr2:234826000-234826200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:234826000-234826200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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