Variant report

Variant	rs11708160
Chromosome Location	chr3:23550746-23550747
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	chr3:23543180..23548543-chr3:23549132..23552642,5	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs11129119	0.89[ASN][1000 genomes]
rs11711072	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs11715841	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718082	0.90[ASN][1000 genomes]
rs11916411	0.94[ASN][1000 genomes]
rs11918529	0.90[ASN][1000 genomes]
rs12386394	0.82[EUR][1000 genomes]
rs12715048	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs13064035	0.96[ASN][1000 genomes]
rs13087861	0.89[CEU][hapmap]
rs1353322	0.88[CEU][hapmap]
rs1498809	0.96[ASN][1000 genomes]
rs1498811	0.96[ASN][1000 genomes]
rs1692612	0.91[ASN][1000 genomes]
rs1692620	0.90[ASN][1000 genomes]
rs1692650	0.93[ASN][1000 genomes]
rs1695200	0.84[ASN][1000 genomes]
rs17194786	0.92[ASN][1000 genomes]
rs2036226	0.92[ASN][1000 genomes]
rs2055310	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2133331	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2173460	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3104244	0.86[ASN][1000 genomes]
rs3111311	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34080387	0.92[ASN][1000 genomes]
rs3817002	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4383458	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4456808	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4484143	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4513393	0.90[ASN][1000 genomes]
rs4635650	0.88[ASN][1000 genomes]
rs4858069	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs4858074	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs4858505	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs4858509	0.88[EUR][1000 genomes]
rs55797660	0.82[EUR][1000 genomes]
rs57137870	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58748418	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60430884	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60632986	0.82[EUR][1000 genomes]
rs62256993	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256994	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6550755	0.82[CEU][hapmap]
rs6550767	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6763329	0.95[ASN][1000 genomes]
rs6763535	0.95[ASN][1000 genomes]
rs6767599	0.89[ASN][1000 genomes]
rs6770079	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6770091	0.89[CEU][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6775232	0.96[ASN][1000 genomes]
rs6776424	0.97[ASN][1000 genomes]
rs6780723	0.92[ASN][1000 genomes]
rs6780787	0.90[ASN][1000 genomes]
rs6795470	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6795968	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs6797907	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798153	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798328	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6805889	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6808513	0.83[ASN][1000 genomes]
rs6810100	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs704533	0.82[ASN][1000 genomes]
rs716456	0.89[CEU][hapmap]
rs73043614	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7612666	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613091	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7614146	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7634117	0.92[ASN][1000 genomes]
rs7636826	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7640308	0.90[ASN][1000 genomes]
rs7644666	0.90[ASN][1000 genomes]
rs7645209	0.89[ASN][1000 genomes]
rs7648443	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7651893	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778475	0.91[ASN][1000 genomes]
rs778476	0.82[ASN][1000 genomes]
rs778477	0.85[EUR][1000 genomes]
rs778480	0.94[ASN][1000 genomes]
rs778482	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778496	0.89[ASN][1000 genomes]
rs778499	0.83[ASN][1000 genomes]
rs778500	0.84[ASN][1000 genomes]
rs778501	0.90[ASN][1000 genomes]
rs778503	0.88[ASN][1000 genomes]
rs778510	0.96[ASN][1000 genomes]
rs778514	0.96[ASN][1000 genomes]
rs778521	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs778523	0.93[ASN][1000 genomes]
rs778526	0.91[ASN][1000 genomes]
rs952134	0.85[CEU][hapmap]
rs9815921	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9821419	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9824359	0.92[ASN][1000 genomes]
rs9830388	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830392	0.90[EUR][1000 genomes]
rs9830742	0.92[ASN][1000 genomes]
rs9836574	0.81[CEU][hapmap]
rs9839738	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9856169	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23526600-23554000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:23528600-23552200	Weak transcription	Ovary	ovary
3	chr3:23536600-23557200	Weak transcription	Left Ventricle	heart
4	chr3:23537400-23551400	Weak transcription	Adipose Nuclei	Adipose
5	chr3:23537400-23559400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:23540400-23560200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:23542800-23559200	Weak transcription	Brain Substantia Nigra	brain
8	chr3:23543000-23552200	Weak transcription	Aorta	Aorta
9	chr3:23543200-23561200	Weak transcription	Psoas Muscle	Psoas
10	chr3:23543400-23552600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:23549800-23550800	Enhancers	Fetal Heart	heart
12	chr3:23550000-23550800	Strong transcription	Primary B cells from cord blood	blood
13	chr3:23550000-23550800	Strong transcription	HSMMtube	muscle
14	chr3:23550600-23560400	Weak transcription	GM12878-XiMat	blood

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