Variant report

Variant	rs10956094
Chromosome Location	chr8:90478557-90478558
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	chr8:90476514..90479734-chr8:90482922..90486651,5	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10094327	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10103261	0.86[EUR][1000 genomes]
rs10103816	0.82[EUR][1000 genomes]
rs10103935	0.86[EUR][1000 genomes]
rs10104048	0.86[EUR][1000 genomes]
rs10216900	0.93[EUR][1000 genomes]
rs1032225	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10956095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10956101	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1155439	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11778295	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11990948	0.81[EUR][1000 genomes]
rs11992806	0.86[EUR][1000 genomes]
rs11996000	0.86[EUR][1000 genomes]
rs12549527	0.82[EUR][1000 genomes]
rs13258962	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13282067	0.93[EUR][1000 genomes]
rs1386648	0.82[EUR][1000 genomes]
rs1487672	0.93[EUR][1000 genomes]
rs1487678	0.86[EUR][1000 genomes]
rs1546745	0.96[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1996853	0.84[EUR][1000 genomes]
rs2338805	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28419680	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28533837	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28601654	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28771098	0.92[EUR][1000 genomes]
rs34059260	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34824390	0.80[EUR][1000 genomes]
rs35285023	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36043792	0.80[EUR][1000 genomes]
rs4571769	0.83[EUR][1000 genomes]
rs4576465	0.86[EUR][1000 genomes]
rs4960972	0.83[EUR][1000 genomes]
rs4960973	0.83[EUR][1000 genomes]
rs4961142	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4961147	0.82[EUR][1000 genomes]
rs56135833	0.83[EUR][1000 genomes]
rs6415479	0.80[EUR][1000 genomes]
rs6470114	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6470130	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6982792	0.87[EUR][1000 genomes]
rs6995460	0.83[EUR][1000 genomes]
rs7016878	0.90[EUR][1000 genomes]
rs719239	0.82[EUR][1000 genomes]
rs7813670	0.85[EUR][1000 genomes]
rs7822577	0.84[EUR][1000 genomes]
rs7835139	0.98[EUR][1000 genomes]
rs7836857	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9297665	0.84[EUR][1000 genomes]
rs9642864	0.93[EUR][1000 genomes]
rs9643174	0.93[EUR][1000 genomes]
rs9987398	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv465735	chr8:89760311-90729507	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv611714	chr8:89760311-90729507	Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	esv2761173	chr8:90404592-90592009	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv984554	chr8:90410700-90501154	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1027327	chr8:90426338-90585108	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1020787	chr8:90437076-90504137	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv967535	chr8:90468032-90479795	Weak transcription Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
8	nsv972191	chr8:90474963-90483818	Weak transcription Enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv1028969	chr8:90475194-90650295	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv528988	chr8:90475375-90608246	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv611720	chr8:90476925-90608246	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10956094	CNGB3	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90458400-90482400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:90478200-90479400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:90478400-90478800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:90478400-90479000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr8:90478400-90479600	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links