Variant report

Variant	rs7016661
Chromosome Location	chr8:39088049-39088050
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	chr8:39079754..39082023-chr8:39086400..39088238,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10088174	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10088458	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10088794	0.81[EUR][1000 genomes]
rs10093393	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10094572	0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs10095244	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs10104527	0.83[JPT][hapmap]
rs10106195	0.81[CEU][hapmap]
rs10108700	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10111607	0.81[CEU][hapmap]
rs10808920	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10958542	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10958543	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11775433	0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11776234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11777253	0.93[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11781014	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs11782591	0.85[EUR][1000 genomes]
rs11786404	0.81[EUR][1000 genomes]
rs11786406	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11786558	0.81[CEU][hapmap]
rs12675132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12679074	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12682638	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13439327	0.81[CEU][hapmap]
rs13439696	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs13439859	0.81[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs28460316	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28649569	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28788037	0.85[EUR][1000 genomes]
rs28795368	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4128223	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4133177	0.81[CEU][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap]
rs4133178	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs4316117	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4515515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537270	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4585712	0.91[TSI][hapmap]
rs4585713	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4587293	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs4733912	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4733913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4733992	0.85[EUR][1000 genomes]
rs4733994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55759907	0.85[EUR][1000 genomes]
rs55817221	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56093547	0.85[EUR][1000 genomes]
rs57822948	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58036010	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6474126	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6980625	0.95[CEU][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap]
rs6981906	0.81[CEU][hapmap]
rs6988280	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6989252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6992204	0.86[TSI][hapmap]
rs7001103	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7013701	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72500200	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73606769	0.81[EUR][1000 genomes]
rs73606771	0.81[EUR][1000 genomes]
rs73606773	0.81[EUR][1000 genomes]
rs73606793	0.85[EUR][1000 genomes]
rs73608630	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73608634	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73608636	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7464434	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7816763	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7843696	0.81[CEU][hapmap]
rs7843723	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7843946	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7845676	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs9801845	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015907	chr8:38967169-39718559	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv539550	chr8:38967169-39718559	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1027443	chr8:38993423-39181079	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv539551	chr8:38993423-39181079	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv428198	chr8:39069309-39405724	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1019752	chr8:39087542-39371410	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7016661	TM2D2	cis	parietal	SCAN
rs7016661	TM2D2	cis	cerebellum	SCAN
rs7016661	ASH2L	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:39076200-39097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:39083200-39097800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr8:39085200-39090400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links