Variant report

Variant	rs12228690
Chromosome Location	chr12:122640007-122640008
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	chr12:122639341..122641993-chr12:122642120..122644689,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10744239	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10773144	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10773171	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10846939	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10846976	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10846977	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11058015	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11058058	0.93[ASN][1000 genomes]
rs11058224	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11058231	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11058236	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11058316	0.87[EUR][1000 genomes]
rs11058323	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12427048	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12427075	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2137200	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175531	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35242277	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35396001	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35822906	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4447210	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4758681	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4758682	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4758683	0.93[EUR][1000 genomes]
rs61955561	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6488994	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6489029	0.85[EUR][1000 genomes]
rs7303129	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7303214	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7311842	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7311871	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7963903	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7964127	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7972527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976422	0.95[ASN][1000 genomes]
rs7979259	0.91[EUR][1000 genomes]
rs925459	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs925460	0.91[ASN][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1038827	chr12:122627371-122687913	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv21424	chr12:122634975-122649886	Weak transcription Enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122627000-122646800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:122629200-122640600	Weak transcription	Primary T cells from cord blood	blood
3	chr12:122629200-122643600	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:122630600-122641200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:122630600-122655600	Weak transcription	Right Ventricle	heart
6	chr12:122630800-122640200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:122634000-122649600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:122636800-122640400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:122636800-122644200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:122636800-122644800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:122639200-122643400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:122640000-122641000	Enhancers	K562	blood

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