Variant report

Variant	rs12298258
Chromosome Location	chr12:66848605-66848606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66840883..66843625-chr12:66848449..66851341,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10219463	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10219465	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10219488	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10219665	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10219742	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506483	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11176200	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11176201	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11176203	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11176218	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12172780	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12172786	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12817668	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818255	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818551	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12818702	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12820901	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2172536	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36154466	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58753311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132670	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7133866	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7134081	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7134178	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7134703	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73137547	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314629	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977115	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1051713	chr12:66745716-66889411	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv832447	chr12:66785814-66990029	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr12:66823200-66859000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:66836200-66849200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:66836200-66849400	Weak transcription	Fetal Kidney	kidney
4	chr12:66836200-66856600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:66836400-66855200	Weak transcription	Placenta	Placenta
6	chr12:66837200-66849200	Weak transcription	Brain Anterior Caudate	brain
7	chr12:66838800-66858400	Weak transcription	Fetal Brain Female	brain
8	chr12:66842800-66849200	Weak transcription	Esophagus	oesophagus
9	chr12:66843400-66849600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:66843800-66857200	Weak transcription	HMEC	breast
11	chr12:66844000-66861600	Weak transcription	Primary T cells from cord blood	blood
12	chr12:66846800-66852000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:66846800-66860200	Weak transcription	Colon Smooth Muscle	Colon

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