Variant report

Variant	rs11722928
Chromosome Location	chr4:82083445-82083446
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	chr4:82073740..82075498-chr4:82082583..82084834,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138669	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10023642	0.88[YRI][hapmap]
rs10029494	0.88[YRI][hapmap]
rs1078980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722019	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11941243	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1348399	0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1443535	0.94[EUR][1000 genomes]
rs1982283	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102818	0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28550691	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3733553	0.93[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs58629505	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6535234	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs751295	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7687935	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7688672	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7696645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9992933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS 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 target site	7 gene(s)	inside rSNPs	diseases
3	nsv829984	chr4:81979988-82113977	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv1822437	chr4:82025743-82118996	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82071000-82085400	Weak transcription	NHDF-Ad	bronchial
2	chr4:82075200-82085400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:82075400-82083600	Weak transcription	Fetal Intestine Large	intestine
4	chr4:82075400-82085800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:82079200-82085400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:82081200-82087200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:82082800-82087200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:82083400-82084200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links