Variant report

Variant	rs12227853
Chromosome Location	chr12:85466292-85466293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10160886	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1031190	1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10506911	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs10506912	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs10779148	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10862955	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11116686	0.84[ASN][1000 genomes]
rs11116692	0.90[YRI][hapmap]
rs11116694	0.98[GIH][hapmap]
rs11116701	0.97[ASN][1000 genomes]
rs11116702	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs11116704	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11116707	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs11116708	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs11116712	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11532387	0.95[ASN][1000 genomes]
rs11609088	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs11612309	0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs11612337	0.83[YRI][hapmap]
rs11615246	0.83[YRI][hapmap]
rs12227986	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12229124	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12229923	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12231122	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs12301980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304556	0.88[EUR][1000 genomes]
rs12814669	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs12817187	0.91[ASN][1000 genomes]
rs1389798	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs1404867	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1404868	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1494500	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494501	0.93[EUR][1000 genomes]
rs1525548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168613	0.95[CEU][hapmap]
rs168615	0.93[EUR][1000 genomes]
rs1690835	0.96[EUR][1000 genomes]
rs17012522	0.99[ASN][1000 genomes]
rs17012533	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs17249909	0.87[YRI][hapmap]
rs1838671	0.99[ASN][1000 genomes]
rs1852148	1.00[CEU][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs1973816	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976270	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2048123	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2056638	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2174754	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2305102	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2404772	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs2404773	0.84[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2660449	0.90[EUR][1000 genomes]
rs2660454	0.89[EUR][1000 genomes]
rs2660455	0.89[EUR][1000 genomes]
rs2660459	0.88[EUR][1000 genomes]
rs2708496	0.90[EUR][1000 genomes]
rs2708498	0.89[EUR][1000 genomes]
rs359992	1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs3765044	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4761074	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4761075	0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4761077	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs4761113	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4761114	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4761115	0.97[ASN][1000 genomes]
rs6539879	0.93[EUR][1000 genomes]
rs6539881	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66617212	0.99[ASN][1000 genomes]
rs7132596	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7133493	0.97[ASN][1000 genomes]
rs7133817	1.00[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7135053	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap]
rs718551	0.87[YRI][hapmap]
rs718553	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7302312	0.88[EUR][1000 genomes]
rs7302315	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs7304576	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7312075	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7316900	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7954110	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956568	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs7962411	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962577	1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7965562	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs796567	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs7974418	1.00[CEU][hapmap]
rs7974623	0.92[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899377	chr12:85157346-85629241	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1040452	chr12:85179586-85747907	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1792335	chr12:85321249-86003609	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv899387	chr12:85427691-85629241	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv455669	chr12:85427691-85638089	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv559653	chr12:85427691-85638089	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv899388	chr12:85427691-85766847	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899389	chr12:85430187-85499132	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv455670	chr12:85465932-85603531	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv559654	chr12:85465932-85603531	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12227853	MYF5	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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