Variant report

Variant	rs12521371
Chromosome Location	chr5:80207763-80207764
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11950254	0.82[EUR][1000 genomes]
rs11956599	0.82[EUR][1000 genomes]
rs12515222	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12515548	0.84[EUR][1000 genomes]
rs12518711	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12521191	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521389	0.82[EUR][1000 genomes]
rs12521539	0.84[EUR][1000 genomes]
rs12522132	0.84[EUR][1000 genomes]
rs12522474	0.82[EUR][1000 genomes]
rs12522866	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13165877	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13168327	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13178429	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13178892	0.82[EUR][1000 genomes]
rs13186354	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs168653	0.81[JPT][hapmap]
rs2112415	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs245340	0.83[ASN][1000 genomes]
rs245341	0.82[ASN][1000 genomes]
rs245348	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs245372	0.82[ASN][1000 genomes]
rs26279	0.84[ASN][1000 genomes]
rs27494	0.84[ASN][1000 genomes]
rs27887	0.84[ASN][1000 genomes]
rs2897298	0.91[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.84[EUR][1000 genomes]
rs32963	0.84[ASN][1000 genomes]
rs32964	0.84[ASN][1000 genomes]
rs32967	0.84[ASN][1000 genomes]
rs32968	0.84[ASN][1000 genomes]
rs34205517	0.82[EUR][1000 genomes]
rs34274010	0.84[EUR][1000 genomes]
rs34560430	0.82[EUR][1000 genomes]
rs34799825	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34816304	0.84[EUR][1000 genomes]
rs34829384	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34976588	0.84[EUR][1000 genomes]
rs35109637	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35856198	0.84[EUR][1000 genomes]
rs35889396	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35967780	0.82[EUR][1000 genomes]
rs36160284	0.82[EUR][1000 genomes]
rs3776976	0.82[EUR][1000 genomes]
rs3776977	0.82[EUR][1000 genomes]
rs3776978	0.82[EUR][1000 genomes]
rs3797898	0.81[EUR][1000 genomes]
rs4293894	0.82[EUR][1000 genomes]
rs55661202	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58825743	0.84[ASN][1000 genomes]
rs59360125	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59568430	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6151888	0.82[EUR][1000 genomes]
rs6151896	0.82[EUR][1000 genomes]
rs6151904	0.82[EUR][1000 genomes]
rs6151907	0.82[EUR][1000 genomes]
rs6151919	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6151923	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66821541	0.82[EUR][1000 genomes]
rs67240890	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6863363	0.84[EUR][1000 genomes]
rs6874051	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6874652	0.82[EUR][1000 genomes]
rs6877065	0.80[EUR][1000 genomes]
rs6891635	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71636248	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72767323	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72767330	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7705816	0.85[ASN][1000 genomes]
rs7717404	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7737445	0.96[ASN][1000 genomes]
rs888867	0.82[EUR][1000 genomes]
rs9293824	0.90[ASN][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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv1799323	chr5:80179312-80219650	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12521371	MSH3	cis	multi-tissue	Pritchard
rs12521371	MSH3	cis	parietal	SCAN
rs12521371	MSH3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80173600-80208000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr5:80180400-80215000	Weak transcription	Fetal Kidney	kidney
3	chr5:80197800-80208200	Weak transcription	Liver	Liver
4	chr5:80207600-80207800	ZNF genes & repeats	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links