Variant report

Variant	rs17006048
Chromosome Location	chr3:19576941-19576942
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	chr3:19525585..19527422-chr3:19576707..19579689,2	MCF-7	breast:
2	chr3:16317176..16319617-chr3:19576040..19578450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270739	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10510495	0.96[ASN][1000 genomes]
rs10514672	1.00[CEU][hapmap]
rs10514673	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap]
rs11543540	0.87[ASN][1000 genomes]
rs11561668	0.94[ASN][1000 genomes]
rs1348231	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1372548	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs1372551	1.00[CEU][hapmap]
rs1442199	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs17005936	1.00[CEU][hapmap]
rs17005937	1.00[CEU][hapmap]
rs17005949	1.00[CEU][hapmap]
rs17005954	1.00[CEU][hapmap]
rs17005967	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs17005972	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs17005976	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17005980	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs17005983	1.00[CEU][hapmap]
rs17005985	1.00[CEU][hapmap]
rs17005998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[ASN][1000 genomes]
rs17006003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs17006010	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs17006054	0.97[ASN][1000 genomes]
rs17006062	0.97[ASN][1000 genomes]
rs4021207	1.00[CEU][hapmap]
rs57272811	0.94[ASN][1000 genomes]
rs57684768	0.91[ASN][1000 genomes]
rs58996643	0.96[ASN][1000 genomes]
rs60546560	0.90[ASN][1000 genomes]
rs60566663	0.97[ASN][1000 genomes]
rs60777133	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs60942804	0.90[ASN][1000 genomes]
rs61579329	0.95[ASN][1000 genomes]
rs6776448	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs6781615	0.83[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs6796647	1.00[CEU][hapmap]
rs6800537	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs6801951	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs7614599	0.82[ASN][1000 genomes]
rs7617994	1.00[CEU][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs7626734	0.96[ASN][1000 genomes]
rs7626907	0.95[ASN][1000 genomes]
rs7649671	0.95[ASN][1000 genomes]
rs7653865	0.87[ASN][1000 genomes]
rs951678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs9841624	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1004602	chr3:19031671-19930052	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536511	chr3:19031671-19930052	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv948636	chr3:19335802-19856585	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv3386719	chr3:19454588-19895807	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv876595	chr3:19512074-19726308	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1009097	chr3:19539647-19787978	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	esv1833163	chr3:19547184-19861406	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	esv1830352	chr3:19549745-19856837	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv1829505	chr3:19554497-19754793	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	esv1833282	chr3:19554497-19849542	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19566600-19577000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:19575000-19578600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:19575600-19577200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:19576200-19578000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr3:19576400-19577600	Enhancers	Adipose Nuclei	Adipose
6	chr3:19576800-19580200	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links