Variant report

Variant	rs7040071
Chromosome Location	chr9:15890098-15890099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNAPC3-1	chr9:15888981-15890761	NONHSAT130281

Extended variants
information (count: 83 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10962193	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10962194	1.00[CHB][hapmap];0.85[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11999303	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12000772	1.00[CHB][hapmap]
rs12005062	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12005485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12005521	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12682932	1.00[CHB][hapmap]
rs12683523	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs12683980	0.86[CHB][hapmap];0.93[AMR][1000 genomes]
rs12684785	0.85[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12684808	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs12685476	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs12685963	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12686591	0.86[CHB][hapmap];0.93[AMR][1000 genomes]
rs1328266	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1328267	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1328268	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1396705	0.85[CHB][hapmap];1.00[EUR][1000 genomes]
rs1536685	0.85[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1536686	0.80[ASN][1000 genomes]
rs1578558	1.00[CHB][hapmap]
rs16933504	1.00[EUR][1000 genomes]
rs16933544	0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16933805	0.85[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs16933814	0.85[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2066291	1.00[CHB][hapmap]
rs2987062	0.80[ASN][1000 genomes]
rs3008684	0.80[ASN][1000 genomes]
rs3008685	0.80[ASN][1000 genomes]
rs34816651	1.00[EUR][1000 genomes]
rs57592105	0.83[ASN][1000 genomes]
rs59779354	0.80[ASN][1000 genomes]
rs59923163	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60354508	0.87[AMR][1000 genomes]
rs60572069	1.00[EUR][1000 genomes]
rs6474950	1.00[JPT][hapmap]
rs6474968	1.00[EUR][1000 genomes]
rs7026090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029375	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7029410	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032595	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7035048	0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs7039881	1.00[CHB][hapmap]
rs7040549	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040580	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040928	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7044984	0.85[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7048479	0.86[CHB][hapmap]
rs73411567	0.87[AMR][1000 genomes]
rs73411570	0.87[AMR][1000 genomes]
rs73411572	0.87[AMR][1000 genomes]
rs73416209	1.00[EUR][1000 genomes]
rs73416213	1.00[EUR][1000 genomes]
rs73416233	1.00[EUR][1000 genomes]
rs73416254	1.00[EUR][1000 genomes]
rs73416261	1.00[EUR][1000 genomes]
rs73416285	1.00[EUR][1000 genomes]
rs73422714	0.83[ASN][1000 genomes]
rs73422737	0.80[ASN][1000 genomes]
rs7388793	1.00[CHB][hapmap]
rs770194	1.00[CHB][hapmap]
rs770198	1.00[CHB][hapmap]
rs770199	1.00[CHB][hapmap]
rs770200	1.00[CHB][hapmap]
rs770201	1.00[CHB][hapmap]
rs770202	1.00[CHB][hapmap]
rs770207	0.82[ASN][1000 genomes]
rs770219	0.80[ASN][1000 genomes]
rs7847946	1.00[EUR][1000 genomes]
rs7852250	1.00[CHB][hapmap]
rs7856304	0.80[ASN][1000 genomes]
rs7861533	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7866472	0.85[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7866699	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867018	1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867521	0.80[ASN][1000 genomes]
rs7869609	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs7870166	0.88[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7870244	0.88[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs809493	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15877000-15903400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:15884200-15891800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:15884200-15892200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:15885800-15892200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:15889000-15890200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr9:15889000-15890800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:15889000-15892800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:15889400-15890200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:15889400-15890400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:15889800-15890400	Enhancers	Osteobl	bone
11	chr9:15889800-15891800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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