Variant report

Variant	rs6870090
Chromosome Location	chr5:74945641-74945642
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	chr5:74944742..74946556-chr5:74948688..74950561,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11948350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11948442	1.00[EUR][1000 genomes]
rs11952534	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11953173	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11953883	1.00[EUR][1000 genomes]
rs11955568	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11955819	0.89[EUR][1000 genomes]
rs11956111	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11956112	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11956755	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11960741	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11960747	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11960771	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1422441	1.00[EUR][1000 genomes]
rs1489	0.94[EUR][1000 genomes]
rs16872590	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs16872661	0.94[EUR][1000 genomes]
rs16872677	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16872683	1.00[EUR][1000 genomes]
rs16872693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1991450	1.00[EUR][1000 genomes]
rs2112348	1.00[EUR][1000 genomes]
rs2112349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2112350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4640773	0.83[EUR][1000 genomes]
rs56832737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57414757	0.89[EUR][1000 genomes]
rs5744617	0.94[EUR][1000 genomes]
rs5744720	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs57512350	0.80[AMR][1000 genomes]
rs57531042	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57670471	1.00[EUR][1000 genomes]
rs58216239	0.89[EUR][1000 genomes]
rs59427628	0.89[EUR][1000 genomes]
rs60385047	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60609097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61516153	0.94[EUR][1000 genomes]
rs6865606	0.89[EUR][1000 genomes]
rs6882452	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6894068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6895148	1.00[EUR][1000 genomes]
rs73120804	0.89[EUR][1000 genomes]
rs73120805	0.89[EUR][1000 genomes]
rs73120807	0.89[EUR][1000 genomes]
rs73120811	0.89[EUR][1000 genomes]
rs73120822	0.89[EUR][1000 genomes]
rs73120824	0.89[EUR][1000 genomes]
rs73120848	0.94[EUR][1000 genomes]
rs73120849	0.94[EUR][1000 genomes]
rs73120850	0.94[EUR][1000 genomes]
rs73122744	0.94[EUR][1000 genomes]
rs73122755	0.94[EUR][1000 genomes]
rs73122770	1.00[EUR][1000 genomes]
rs73122771	1.00[EUR][1000 genomes]
rs73122772	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124734	1.00[EUR][1000 genomes]
rs73124747	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7724771	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74921800-74964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:74944800-74947400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:74944800-74952200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:74945000-74946800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:74945000-74947000	Weak transcription	Fetal Intestine Small	intestine
6	chr5:74945000-74947200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:74945000-74962800	Weak transcription	Fetal Intestine Large	intestine
8	chr5:74945600-74946600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links