Variant report

Variant	rs4141552
Chromosome Location	chr6:54759929-54759930
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	chr6:54758702..54760512-chr6:54764567..54767361,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10485136	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1115159	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12525787	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12662124	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1393776	0.83[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs148109	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1503140	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1503146	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963697	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2064432	0.94[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2179786	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs239790	0.82[CHD][hapmap]
rs239794	0.83[CHD][hapmap]
rs239796	0.83[CHD][hapmap]
rs239837	0.83[CHD][hapmap]
rs239850	0.87[ASN][1000 genomes]
rs239852	0.80[YRI][hapmap]
rs239854	0.87[ASN][1000 genomes]
rs2816811	0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4712081	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6459035	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6902245	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6902422	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6908170	0.91[EUR][1000 genomes]
rs6922186	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6926997	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6929930	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6939778	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72645372	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7453866	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7741915	0.83[CHD][hapmap]
rs7744592	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7746374	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7764641	0.80[AMR][1000 genomes]
rs9296771	0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs932452	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9349740	0.90[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9357822	0.82[EUR][1000 genomes]
rs9367597	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9367608	0.82[CHB][hapmap]
rs9370332	0.84[CHB][hapmap]
rs9370333	0.84[CHB][hapmap]
rs9370344	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9370345	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9382396	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9382397	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9382398	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9382402	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9382403	0.95[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9382404	0.80[AMR][1000 genomes]
rs9382408	0.80[AMR][1000 genomes]
rs9382442	0.81[CHB][hapmap]
rs9396006	0.94[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9396007	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9396036	0.93[CHB][hapmap]
rs9475068	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9475069	0.90[EUR][1000 genomes]
rs9475078	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9475081	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs960834	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs960835	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs988913	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
2	chr6:54744400-54761000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:54757200-54763000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:54757800-54760600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:54757800-54763200	Weak transcription	NHEK	skin
6	chr6:54758000-54761200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:54758000-54769400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:54758000-54775000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:54758400-54761000	Weak transcription	HMEC	breast
10	chr6:54759200-54761000	Weak transcription	Fetal Intestine Small	intestine
11	chr6:54759200-54763000	Weak transcription	Fetal Intestine Large	intestine
12	chr6:54759600-54760600	Weak transcription	Rectal Mucosa Donor 31	rectum

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