Variant report

Variant	rs6880562
Chromosome Location	chr5:112657560-112657561
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	chr5:112628328..112630254-chr5:112656025..112657722,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10038521	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10051115	0.95[ASN][1000 genomes]
rs10053341	0.86[ASN][1000 genomes]
rs10061462	0.95[ASN][1000 genomes]
rs10434754	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10477490	0.95[ASN][1000 genomes]
rs1157696	0.84[ASN][1000 genomes]
rs13154300	0.90[ASN][1000 genomes]
rs13159509	0.90[ASN][1000 genomes]
rs13164135	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13164326	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13170435	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13171482	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13174075	0.86[ASN][1000 genomes]
rs13174151	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13174206	0.90[ASN][1000 genomes]
rs13177853	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13180516	0.90[ASN][1000 genomes]
rs13180522	0.95[ASN][1000 genomes]
rs13181534	0.95[ASN][1000 genomes]
rs13181732	0.90[ASN][1000 genomes]
rs13181944	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13183383	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13184538	0.90[ASN][1000 genomes]
rs13187823	0.90[ASN][1000 genomes]
rs13189050	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13189910	0.95[ASN][1000 genomes]
rs1602862	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17325307	0.88[ASN][1000 genomes]
rs17325503	0.86[ASN][1000 genomes]
rs17325825	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17327964	0.90[ASN][1000 genomes]
rs17388260	0.90[ASN][1000 genomes]
rs17389165	0.90[ASN][1000 genomes]
rs1838206	0.90[ASN][1000 genomes]
rs1922678	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1922679	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34316732	0.95[ASN][1000 genomes]
rs34558181	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34682492	0.95[ASN][1000 genomes]
rs34951736	0.90[ASN][1000 genomes]
rs35359071	0.90[ASN][1000 genomes]
rs35886114	0.95[ASN][1000 genomes]
rs4438866	0.90[ASN][1000 genomes]
rs58268366	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6594706	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6594713	0.95[ASN][1000 genomes]
rs6594714	0.95[ASN][1000 genomes]
rs6594715	0.95[ASN][1000 genomes]
rs6594716	0.95[ASN][1000 genomes]
rs66572866	0.90[ASN][1000 genomes]
rs67320720	0.90[ASN][1000 genomes]
rs67693032	0.90[ASN][1000 genomes]
rs6870401	0.95[ASN][1000 genomes]
rs6871934	0.90[ASN][1000 genomes]
rs6872490	0.86[ASN][1000 genomes]
rs6874175	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883102	0.88[ASN][1000 genomes]
rs6887482	0.95[ASN][1000 genomes]
rs6887914	0.90[ASN][1000 genomes]
rs6889489	0.86[ASN][1000 genomes]
rs6890874	0.90[ASN][1000 genomes]
rs6896843	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71577442	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs71577447	0.90[ASN][1000 genomes]
rs71577448	0.90[ASN][1000 genomes]
rs72792189	0.81[ASN][1000 genomes]
rs7701895	0.88[ASN][1000 genomes]
rs7709646	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7714221	0.86[ASN][1000 genomes]
rs7714760	0.95[ASN][1000 genomes]
rs7717630	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7718616	0.90[ASN][1000 genomes]
rs7720414	0.86[ASN][1000 genomes]
rs7725712	0.95[ASN][1000 genomes]
rs7727056	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7727501	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7729269	0.95[ASN][1000 genomes]
rs7731231	0.95[ASN][1000 genomes]
rs7734576	0.95[ASN][1000 genomes]
rs7737512	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112648800-112666600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:112653000-112673600	Weak transcription	Fetal Kidney	kidney
3	chr5:112655000-112657600	Enhancers	Liver	Liver
4	chr5:112655800-112658600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:112655800-112658800	Weak transcription	Placenta	Placenta
6	chr5:112656000-112666200	Weak transcription	HMEC	breast
7	chr5:112656200-112661200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:112656600-112666600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:112657400-112669200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links