Variant report

Variant	rs6762708
Chromosome Location	chr3:156691604-156691605
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	chr3:156689383..156692274-chr3:156693134..156695144,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10212230	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs10936040	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs10936043	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs11914959	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs12634915	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs12638253	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs13070271	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs13088978	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs1319418	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs1320011	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1384538	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs1574980	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1995425	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2054880	0.83[JPT][hapmap]
rs2321290	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs2321291	0.88[CEU][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs2321292	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2321293	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2321455	0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2874488	0.94[CEU][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2874494	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2874495	0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs343994	0.83[JPT][hapmap]
rs344073	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs344079	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs344080	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs344082	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs344084	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs344087	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs416600	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4234316	0.88[CEU][hapmap]
rs4315647	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4458324	0.82[AMR][1000 genomes]
rs453219	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4589888	0.81[ASN][1000 genomes]
rs4680311	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680312	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs4680313	0.88[EUR][1000 genomes]
rs4680314	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680317	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs6441101	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6765353	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6780427	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs6780475	0.91[EUR][1000 genomes]
rs6783162	0.83[EUR][1000 genomes]
rs6784421	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs6803064	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7615304	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs7622309	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7637701	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7638330	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7638625	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs873337	0.88[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs9814813	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs9826073	0.85[EUR][1000 genomes]
rs9837038	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs9844054	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs9847187	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs9862338	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9863643	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9865905	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs9867621	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs9870137	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9871817	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs9875585	0.84[ASN][1000 genomes]
rs9876010	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs9876148	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs987724	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs9878585	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs9882009	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9883439	0.88[CEU][hapmap];0.90[EUR][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	nsv829765	chr3:156568263-156718496	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv592120	chr3:156626091-156691604	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6762708	LEKR1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156691400-156692400	Enhancers	HMEC	breast
2	chr3:156691400-156692400	Enhancers	NHEK	skin
3	chr3:156691400-156692800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:156691600-156692200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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