Variant report

Variant	rs11838338
Chromosome Location	chr12:1989355-1989356
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	chr12:1962744..1965202-chr12:1987725..1990187,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151062	Chromatin interaction

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

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

rs_ID	r²[population]
rs11829061	1.00[CEU][hapmap];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]
rs12298882	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12300820	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2013095	0.81[JPT][hapmap]
rs4765854	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765855	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs4765856	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[EUR][1000 genomes]
rs55779143	0.82[EUR][1000 genomes]
rs58041839	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60708075	0.89[EUR][1000 genomes]
rs60945277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61085710	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61386831	0.89[EUR][1000 genomes]
rs61457024	0.89[EUR][1000 genomes]
rs68074245	0.82[EUR][1000 genomes]
rs7297190	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032415	0.84[EUR][1000 genomes]
rs73032423	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73032427	0.86[EUR][1000 genomes]
rs73032431	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032438	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73032440	0.89[EUR][1000 genomes]
rs73032452	0.89[EUR][1000 genomes]
rs73036228	0.89[EUR][1000 genomes]
rs73036240	0.89[EUR][1000 genomes]
rs73038172	0.84[EUR][1000 genomes]
rs73038195	0.80[EUR][1000 genomes]
rs7308134	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737102	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758160	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[EUR][1000 genomes]
rs7957635	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964656	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966806	0.90[EUR][1000 genomes]
rs7969511	0.85[EUR][1000 genomes]
rs7980286	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs9669070	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv898599	chr12:1942752-1989355	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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	chr12:1981000-1992000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:1989000-1990600	Enhancers	Fetal Muscle Leg	muscle
3	chr12:1989000-1991400	Enhancers	Fetal Muscle Trunk	muscle
4	chr12:1989200-1989400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:1989200-1989400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:1989200-1989400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:1989200-1990200	Bivalent Enhancer	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links