Variant report

Variant	rs10858425
Chromosome Location	chr12:86800054-86800055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10431399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs10735250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10745407	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs10745408	0.84[CEU][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.93[TSI][hapmap]
rs10745416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10745419	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10776955	0.84[CEU][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs10776961	0.88[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10776966	0.88[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs10776968	0.91[AMR][1000 genomes]
rs10776969	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs10776971	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs10776976	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10776977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10858408	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs10858412	0.95[CHD][hapmap];0.95[JPT][hapmap]
rs10858419	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10858427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10858428	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap]
rs10858436	0.82[YRI][hapmap]
rs10858444	0.83[JPT][hapmap];0.85[YRI][hapmap]
rs11103983	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12317113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs12578669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12582690	0.95[JPT][hapmap]
rs1463749	0.90[TSI][hapmap]
rs1493415	0.82[JPT][hapmap]
rs1698787	0.84[JPT][hapmap]
rs1922742	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1922749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1955399	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2091818	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap]
rs2405923	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2405925	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs2405928	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs2405930	0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs2406115	0.84[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs2406116	0.84[CEU][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs2406118	0.84[CEU][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs2406122	0.84[CEU][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs2406123	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs2406127	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs2406128	0.84[JPT][hapmap]
rs2406160	0.85[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap]
rs2452807	0.84[JPT][hapmap]
rs2465144	0.84[JPT][hapmap]
rs2471560	0.86[GIH][hapmap];0.84[JPT][hapmap]
rs2471568	0.84[JPT][hapmap]
rs2471569	0.84[JPT][hapmap]
rs2897278	0.81[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs2897280	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs4265650	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs4370997	0.83[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap]
rs4399378	0.82[YRI][hapmap]
rs4628748	0.88[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4842483	0.82[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs6538025	0.86[GIH][hapmap];0.84[JPT][hapmap]
rs6538029	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs6538033	0.84[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs6538042	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs6538046	0.86[YRI][hapmap]
rs7135177	0.84[CEU][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap]
rs7137308	0.90[TSI][hapmap]
rs7139324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap]
rs7297574	0.89[YRI][hapmap]
rs7299319	0.83[ASW][hapmap];0.88[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs7303796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7953196	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs7957560	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs7963659	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap]
rs7964553	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs7972484	0.84[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs7973543	0.93[YRI][hapmap]
rs7973773	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs7977689	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs839104	0.86[GIH][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap]
rs839105	0.86[GIH][hapmap]
rs839168	0.84[JPT][hapmap]
rs839170	0.84[JPT][hapmap]
rs839171	0.84[GIH][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap]
rs844434	0.84[JPT][hapmap]

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	esv2754127	chr12:86723232-87576932	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3321758	chr12:86799321-86800569	Bivalent/Poised TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10858425	PPFIA2	cis	cerebellum	SCAN
rs10858425	SNORA20	trans	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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