Variant report

Variant	rs778476
Chromosome Location	chr3:23500996-23500997
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	chr3:23489983..23492292-chr3:23500438..23503341,2	MCF-7	breast:

Extended variants
information (count: 138 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1027379	0.82[JPT][hapmap]
rs11129119	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11708160	0.82[ASN][1000 genomes]
rs11715841	0.94[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11718082	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11916411	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11918529	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12493361	0.81[JPT][hapmap]
rs12629848	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs12715047	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13064035	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13321359	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13326048	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1498809	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1498811	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1692612	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1692617	0.96[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1692620	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1692622	0.89[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs1692650	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1692651	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1692652	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1695170	0.84[EUR][1000 genomes]
rs1695171	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1695181	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1695200	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17194786	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1874235	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1908773	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2036226	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2055310	0.93[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2133331	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs2172828	0.81[JPT][hapmap]
rs2173460	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs2173461	0.86[ASN][1000 genomes]
rs2359759	0.96[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2359763	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3104243	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3104244	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3111311	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.84[ASN][1000 genomes]
rs34080387	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3817002	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4513393	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4635650	0.85[EUR][1000 genomes]
rs4858071	0.83[EUR][1000 genomes]
rs4858072	0.82[EUR][1000 genomes]
rs4858077	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4858496	0.81[JPT][hapmap]
rs4858497	0.95[JPT][hapmap];0.87[MEX][hapmap]
rs4858500	0.81[JPT][hapmap]
rs4858502	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs4858504	0.88[EUR][1000 genomes]
rs4858506	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs4858508	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4858511	0.81[EUR][1000 genomes]
rs57137870	0.81[ASN][1000 genomes]
rs58748418	0.81[ASN][1000 genomes]
rs60581845	0.88[EUR][1000 genomes]
rs6550756	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs6763329	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6763535	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6767599	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6769173	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6775232	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6776424	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6780723	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6780787	0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6784195	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6796840	0.96[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6797907	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs6798153	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs6798328	0.82[ASN][1000 genomes]
rs6804123	0.81[JPT][hapmap]
rs6808513	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs704533	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs704534	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs716457	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs7612666	0.82[ASN][1000 genomes]
rs7613091	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7631334	1.00[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7634117	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7640308	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7644666	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7645209	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs778459	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778460	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs778461	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778462	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs778467	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778468	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778470	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778471	0.85[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs778475	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778477	0.83[ASN][1000 genomes]
rs778480	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778482	0.82[ASN][1000 genomes]
rs778484	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778485	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778486	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs778487	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778488	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs778494	1.00[CEU][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes]
rs778496	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs778499	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778500	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778501	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778503	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778506	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778507	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778508	1.00[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778510	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778514	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778521	0.84[GIH][hapmap]
rs778523	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778526	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9824359	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9825778	1.00[CEU][hapmap];0.80[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9826089	0.88[EUR][1000 genomes]
rs9826647	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9827507	0.83[EUR][1000 genomes]
rs9830388	0.94[CHB][hapmap]
rs9830742	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9840820	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9846398	0.83[MEX][hapmap]
rs9847027	0.81[JPT][hapmap]
rs9849176	0.88[JPT][hapmap]
rs9849424	0.87[EUR][1000 genomes]
rs9853489	0.90[JPT][hapmap];0.83[MEX][hapmap]
rs9856169	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9859515	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9859651	1.00[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9873317	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9874082	0.81[JPT][hapmap]
rs9874519	0.84[AMR][1000 genomes];0.87[EUR][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	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	nsv876625	chr3:23390301-23509597	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23491800-23501200	Weak transcription	Brain Substantia Nigra	brain
2	chr3:23494400-23501000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:23494400-23502000	Weak transcription	HSMMtube	muscle
4	chr3:23494400-23504200	Weak transcription	Thymus	Thymus
5	chr3:23496600-23505000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:23497200-23501000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:23497200-23501400	Weak transcription	Psoas Muscle	Psoas
8	chr3:23497400-23501000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:23497400-23502600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:23497600-23501400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:23498000-23501200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:23498200-23501000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:23498200-23516200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:23498400-23501200	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:23498600-23506600	Weak transcription	Primary B cells from cord blood	blood
16	chr3:23500200-23501200	Enhancers	NHLF	lung
17	chr3:23500400-23502800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:23500400-23503000	Enhancers	NHDF-Ad	bronchial
19	chr3:23500600-23501200	Enhancers	Fetal Stomach	stomach
20	chr3:23500600-23501800	Enhancers	Colon Smooth Muscle	Colon
21	chr3:23500800-23501800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:23500800-23501800	Enhancers	Stomach Smooth Muscle	stomach
23	chr3:23500800-23502000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:23500800-23502200	Enhancers	Brain Hippocampus Middle	brain
25	chr3:23500800-23502200	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links