Variant report

Variant	rs9292854
Chromosome Location	chr5:42611820-42611821
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:41924043..41926893-chr5:42611751..42613531,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151876	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10041108	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10069861	1.00[ASN][1000 genomes]
rs10440649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10941582	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10941588	1.00[ASN][1000 genomes]
rs1109882	1.00[ASN][1000 genomes]
rs11948120	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948453	0.83[CEU][hapmap];0.96[EUR][1000 genomes]
rs11957404	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514437	1.00[ASN][1000 genomes]
rs13156541	1.00[CHB][hapmap]
rs13163126	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13168440	1.00[CHB][hapmap]
rs13171019	1.00[ASN][1000 genomes]
rs13171720	1.00[CHB][hapmap]
rs13173465	0.93[EUR][1000 genomes]
rs13175765	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13182117	1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13184352	1.00[CHB][hapmap]
rs13188386	1.00[CHB][hapmap]
rs13354167	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17574527	1.00[CHB][hapmap]
rs17574616	1.00[CHB][hapmap]
rs17575164	1.00[CHB][hapmap]
rs17636762	1.00[CHB][hapmap]
rs28943882	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34159518	1.00[ASN][1000 genomes]
rs35164552	1.00[ASN][1000 genomes]
rs35893798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129472	1.00[CHB][hapmap]
rs4242122	1.00[ASN][1000 genomes]
rs4242123	1.00[ASN][1000 genomes]
rs4242124	1.00[ASN][1000 genomes]
rs4292454	1.00[CHB][hapmap]
rs4554233	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs4866791	0.83[CEU][hapmap];0.94[EUR][1000 genomes]
rs4866793	1.00[ASN][1000 genomes]
rs4866955	1.00[ASN][1000 genomes]
rs4866956	1.00[ASN][1000 genomes]
rs4866957	1.00[ASN][1000 genomes]
rs5025611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6413428	1.00[CHB][hapmap]
rs6414898	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6451634	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6451641	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6451643	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs68070657	0.80[EUR][1000 genomes]
rs6863381	1.00[CHB][hapmap]
rs6871947	1.00[ASN][1000 genomes]
rs6873340	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6894403	1.00[ASN][1000 genomes]
rs7444761	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7702524	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703669	1.00[CHB][hapmap]
rs7709370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709790	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7718962	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1027023	chr5:42610250-42654999	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42592000-42614400	Weak transcription	Aorta	Aorta
2	chr5:42601200-42612800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:42606800-42613200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:42607000-42621000	Weak transcription	Left Ventricle	heart
5	chr5:42609200-42613600	Enhancers	Liver	Liver
6	chr5:42610200-42620600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:42610800-42626800	Weak transcription	Pancreas	Pancrea
8	chr5:42611000-42612400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:42611200-42612800	Weak transcription	Psoas Muscle	Psoas
10	chr5:42611800-42616200	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links