Variant report

Variant	rs12298882
Chromosome Location	chr12:1993258-1993259
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	chr12:1982062..1983660-chr12:1991935..1993547,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10848584	0.91[JPT][hapmap]
rs11829061	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11838338	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12307334	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs12311729	0.87[CHB][hapmap];0.91[CHD][hapmap]
rs12312103	0.87[CHB][hapmap]
rs1990233	0.90[JPT][hapmap]
rs2887632	0.83[CHB][hapmap]
rs4765854	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs55779143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58041839	0.82[EUR][1000 genomes]
rs60945277	0.82[EUR][1000 genomes]
rs61085710	0.82[EUR][1000 genomes]
rs68074245	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297190	0.85[CEU][hapmap]
rs7308134	0.85[CEU][hapmap]
rs737102	0.85[CEU][hapmap]
rs740458	0.91[JPT][hapmap]
rs7957635	0.85[CEU][hapmap]
rs7964656	0.84[EUR][1000 genomes]
rs7980286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1045447	chr12:1959333-1993612	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1046388	chr12:1964846-2034887	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1043329	chr12:1986238-2034887	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1989400-1995600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:1990200-1994200	Weak transcription	K562	blood
3	chr12:1993000-1997000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:1993200-1993400	Bivalent Enhancer	Fetal Stomach	stomach
5	chr12:1993200-1993400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
6	chr12:1993200-1993600	Enhancers	Fetal Muscle Leg	muscle
7	chr12:1993200-1993800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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