Variant report

Variant	rs750688
Chromosome Location	chr3:159358778-159358779
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	chr3:159358374..159361100-chr3:159366221..159368594,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10154893	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10513539	1.00[GIH][hapmap]
rs11919032	1.00[GIH][hapmap]
rs11921824	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11921827	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107648	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs13434009	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1343824	0.84[ASN][1000 genomes]
rs1347671	0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1347672	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1356927	0.83[JPT][hapmap]
rs1437519	0.83[JPT][hapmap]
rs1437520	0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1581342	0.84[JPT][hapmap]
rs16830510	0.83[JPT][hapmap]
rs16830519	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs16830523	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs16830532	1.00[GIH][hapmap]
rs16830534	0.85[ASN][1000 genomes]
rs16830546	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs16830575	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830579	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16830581	1.00[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830589	0.88[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1816621	0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1816622	1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1962890	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1978830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28434644	0.99[ASN][1000 genomes]
rs28743043	0.83[ASN][1000 genomes]
rs2886621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4494974	0.90[ASN][1000 genomes]
rs59556163	0.84[ASN][1000 genomes]
rs61018732	0.84[ASN][1000 genomes]
rs61373569	0.84[ASN][1000 genomes]
rs6772245	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6789368	1.00[GIH][hapmap]
rs73012253	0.85[ASN][1000 genomes]
rs7630289	1.00[GIH][hapmap]
rs9290046	0.88[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9290047	0.88[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9809076	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809681	0.83[JPT][hapmap]
rs9819000	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9819080	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs9824363	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs9826417	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9829310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9831125	0.83[TSI][hapmap]
rs9832970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9833713	0.83[JPT][hapmap]
rs9842465	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9848763	0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs9848897	0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs9849705	0.82[ASN][1000 genomes]
rs9851700	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860690	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs9866650	1.00[GIH][hapmap]
rs9867212	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870872	0.85[ASN][1000 genomes]
rs9877425	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9879792	1.00[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881603	0.83[JPT][hapmap]
rs9882328	0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs9883498	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 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	chr3:159356200-159363200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:159356400-159379800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:159358000-159358800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr3:159358000-159358800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:159358000-159359000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:159358200-159359000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:159358400-159358800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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