Variant report

Variant	rs12520080
Chromosome Location	chr5:146709922-146709923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10041697	0.82[JPT][hapmap]
rs10042298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10070932	0.87[JPT][hapmap]
rs10079191	0.81[JPT][hapmap]
rs10477336	0.87[JPT][hapmap]
rs10515580	0.87[JPT][hapmap]
rs10515581	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10515582	0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10515583	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11167988	0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11167989	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs11748615	0.87[JPT][hapmap]
rs11954789	0.87[JPT][hapmap]
rs12513884	0.84[AMR][1000 genomes]
rs12514269	0.82[JPT][hapmap]
rs12514302	0.86[CHB][hapmap]
rs12518250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12519887	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12520257	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12520436	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12522616	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12651731	0.93[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes]
rs12659468	0.88[JPT][hapmap]
rs13170279	0.82[JPT][hapmap]
rs1432838	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1432857	0.85[CHB][hapmap]
rs1544816	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17106458	0.87[JPT][hapmap]
rs17106470	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17106482	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17106492	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17106560	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17106572	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes]
rs17106575	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs17106590	0.84[AMR][1000 genomes]
rs17106592	0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs17106597	0.93[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs17106606	0.84[AMR][1000 genomes]
rs1895566	1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2288805	0.85[CHB][hapmap]
rs2288809	0.84[CHB][hapmap]
rs2400295	0.87[JPT][hapmap]
rs2895681	0.84[AMR][1000 genomes]
rs3213857	0.85[CHB][hapmap]
rs3749721	0.86[CHB][hapmap];0.84[AMR][1000 genomes]
rs3792837	0.86[CHB][hapmap]
rs3805533	0.86[CHB][hapmap];0.84[AMR][1000 genomes]
rs3805534	0.93[CHB][hapmap]
rs3805535	0.92[CHB][hapmap]
rs3805543	0.85[CHB][hapmap]
rs3805544	0.83[CHB][hapmap]
rs4642416	0.84[AMR][1000 genomes]
rs4705164	0.82[JPT][hapmap]
rs4705165	0.87[JPT][hapmap]
rs4705166	0.87[JPT][hapmap]
rs6872292	0.88[JPT][hapmap]
rs6884181	0.87[JPT][hapmap]
rs7707452	0.87[JPT][hapmap]
rs7714240	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs918797	0.81[JPT][hapmap]
rs918798	0.87[JPT][hapmap]
rs972302	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs9885145	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr5:146703200-146711800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:146703600-146716400	Weak transcription	Ovary	ovary
3	chr5:146703800-146711400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:146707000-146716400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:146707400-146716400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:146707600-146725600	Weak transcription	Pancreas	Pancrea
7	chr5:146707800-146712000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:146709000-146711600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:146709800-146710000	Enhancers	Brain Germinal Matrix	brain
10	chr5:146709800-146710000	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links