Variant report

Variant	rs932452
Chromosome Location	chr6:54801928-54801929
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	chr6:54793235..54795806-chr6:54798273..54802120,4	MCF-7	breast:
2	chr6:54571628..54573912-chr6:54800682..54803427,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10485136	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1115159	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12525787	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12662124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1393776	0.90[CEU][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs148109	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs1503140	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1503146	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1503147	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2064432	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2179786	0.81[CHB][hapmap]
rs2816811	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs4141552	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]
rs4712081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6459035	0.93[EUR][1000 genomes]
rs6902245	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6902422	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6908170	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6922186	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6926997	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6929930	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6939778	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72645372	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7453866	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7739399	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7744592	0.84[EUR][1000 genomes]
rs7746374	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7764641	0.81[AMR][1000 genomes]
rs9296771	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349740	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs9357840	0.89[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs9367597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9367602	0.89[ASN][1000 genomes]
rs9370332	0.81[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]
rs9370333	0.81[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]
rs9370344	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9370345	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9370350	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9370351	0.89[ASN][1000 genomes]
rs9370352	0.89[ASN][1000 genomes]
rs9382396	0.91[EUR][1000 genomes]
rs9382397	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9382398	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382402	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382403	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9382404	0.81[AMR][1000 genomes]
rs9382408	0.81[AMR][1000 genomes]
rs9382411	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9396006	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9396007	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9396013	0.88[ASN][1000 genomes]
rs9396036	0.87[CHB][hapmap]
rs9475068	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475069	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475078	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9475081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475106	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9475107	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs960834	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs960835	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs988913	0.90[CEU][hapmap];0.88[MEX][hapmap];0.85[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:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54785600-54805000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:54789800-54810200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:54797000-54811800	Weak transcription	Esophagus	oesophagus
4	chr6:54797600-54804600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:54798000-54804600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:54798800-54804800	Weak transcription	Fetal Intestine Large	intestine
7	chr6:54798800-54815600	Weak transcription	Fetal Intestine Small	intestine
8	chr6:54800400-54802200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:54800400-54807600	Weak transcription	Small Intestine	intestine
10	chr6:54800600-54802600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:54801000-54805000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:54801200-54804400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:54801600-54802200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:54801600-54802200	Weak transcription	HMEC	breast
15	chr6:54801600-54802200	Weak transcription	NHEK	skin
16	chr6:54801600-54804800	Weak transcription	Hela-S3	cervix

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