Variant report

Variant	rs12778446
Chromosome Location	chr10:90223879-90223880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10509544	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10736353	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10736355	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10749585	0.80[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes]
rs10749586	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10749587	0.98[ASN][1000 genomes]
rs10749588	0.98[ASN][1000 genomes]
rs10788595	0.87[EUR][1000 genomes]
rs10788597	0.95[EUR][1000 genomes]
rs10788601	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10788604	0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10788605	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10887820	0.80[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes]
rs10887827	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10887829	0.80[CHB][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11202750	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1183901	0.81[CHB][hapmap]
rs12266064	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1325907	0.80[CHB][hapmap]
rs1409134	0.80[CHB][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1426620	0.87[EUR][1000 genomes]
rs1935578	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1935580	0.95[EUR][1000 genomes]
rs2153856	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2437872	0.93[JPT][hapmap]
rs2437878	0.80[CHB][hapmap]
rs2477957	1.00[JPT][hapmap]
rs2488271	0.81[CHB][hapmap]
rs2576174	0.80[CHB][hapmap]
rs2576179	0.81[CHB][hapmap]
rs2765444	0.81[CHB][hapmap]
rs4403718	0.95[ASN][1000 genomes]
rs6586130	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6586134	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7077182	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7096710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs725683	0.80[CHB][hapmap]
rs725684	0.80[CHB][hapmap]
rs7895199	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7897033	0.88[EUR][1000 genomes]
rs7902230	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7904229	0.98[ASN][1000 genomes]
rs7907866	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7913372	0.86[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7916937	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7917100	0.84[YRI][hapmap]
rs7919420	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7922053	0.91[AMR][1000 genomes];0.96[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	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90193800-90227600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:90216800-90227400	Weak transcription	Ovary	ovary
3	chr10:90218400-90226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:90220200-90226800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:90221000-90227400	Weak transcription	Right Atrium	heart
6	chr10:90221000-90227400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:90223600-90224000	Enhancers	Pancreatic Islets	Pancreatic Islet

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