Variant report

Variant	rs4842483
Chromosome Location	chr12:86764618-86764619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10431399	0.82[CEU][hapmap]
rs10745407	0.91[CEU][hapmap]
rs10745408	0.91[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs10776955	0.91[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs10776957	0.94[EUR][1000 genomes]
rs10776959	0.95[EUR][1000 genomes]
rs10776961	0.95[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs10776966	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776968	0.95[EUR][1000 genomes]
rs10776969	0.95[CEU][hapmap]
rs10776971	0.82[CEU][hapmap];0.95[TSI][hapmap]
rs10858408	0.91[CEU][hapmap]
rs10858419	0.99[EUR][1000 genomes]
rs10858425	0.82[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs10858427	0.82[CEU][hapmap]
rs10858428	0.82[CEU][hapmap]
rs12317113	0.82[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs12578669	0.82[CEU][hapmap]
rs1463749	0.86[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1493415	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs1493416	0.93[EUR][1000 genomes]
rs1532262	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs1552839	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs1602848	0.83[EUR][1000 genomes]
rs1602850	0.93[EUR][1000 genomes]
rs1689340	0.82[CEU][hapmap]
rs1689357	0.87[EUR][1000 genomes]
rs1698787	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs1922749	0.86[CEU][hapmap]
rs1948448	0.92[EUR][1000 genomes]
rs2091818	0.93[TSI][hapmap]
rs2131565	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs2405923	0.86[CEU][hapmap]
rs2405925	0.95[CEU][hapmap]
rs2405928	0.95[CEU][hapmap]
rs2405930	0.96[EUR][1000 genomes]
rs2405933	0.82[EUR][1000 genomes]
rs2406115	0.91[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs2406116	0.91[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2406117	0.94[EUR][1000 genomes]
rs2406118	0.91[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2406119	0.94[EUR][1000 genomes]
rs2406122	0.91[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2406123	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs2406127	0.91[CEU][hapmap]
rs2452806	0.86[CEU][hapmap];0.93[EUR][1000 genomes]
rs2452807	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs2452811	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs2452815	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs2465143	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs2465144	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs2465146	0.93[EUR][1000 genomes]
rs2465147	0.92[EUR][1000 genomes]
rs2465149	0.82[CEU][hapmap]
rs2471560	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs2471564	0.82[CEU][hapmap]
rs2471568	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs2471569	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs2471570	0.90[EUR][1000 genomes]
rs2897278	0.85[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs2897280	0.91[CEU][hapmap]
rs4265650	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs4334094	0.94[EUR][1000 genomes]
rs4503614	0.94[EUR][1000 genomes]
rs4628748	0.95[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs6538025	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs6538028	0.85[CEU][hapmap]
rs6538029	0.91[CEU][hapmap]
rs6538031	0.95[EUR][1000 genomes]
rs6538032	0.95[EUR][1000 genomes]
rs6538033	0.91[CEU][hapmap];0.90[TSI][hapmap]
rs6538038	0.80[EUR][1000 genomes]
rs7134946	0.88[EUR][1000 genomes]
rs7135177	0.91[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs7135733	0.94[EUR][1000 genomes]
rs7135741	0.94[EUR][1000 genomes]
rs7137308	0.86[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7299319	0.95[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs7310186	0.96[EUR][1000 genomes]
rs7953196	0.90[CEU][hapmap]
rs7957560	0.91[CEU][hapmap]
rs7964553	0.91[CEU][hapmap]
rs7972484	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs7973773	0.91[CEU][hapmap]
rs7977689	0.83[CEU][hapmap]
rs839104	0.86[CEU][hapmap];0.88[TSI][hapmap]
rs839105	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs839148	0.82[CEU][hapmap]
rs839157	0.86[CEU][hapmap];0.88[TSI][hapmap]
rs839159	0.86[CEU][hapmap]
rs839163	0.83[EUR][1000 genomes]
rs839164	0.83[EUR][1000 genomes]
rs839165	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs839168	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs839170	0.86[CEU][hapmap]
rs839171	0.86[CEU][hapmap];0.88[TSI][hapmap]
rs844435	0.86[CEU][hapmap];0.88[TSI][hapmap]
rs863392	0.82[CEU][hapmap]
rs863395	0.86[CEU][hapmap];0.88[TSI][hapmap]
rs865138	0.82[CEU][hapmap]
rs9919783	0.96[EUR][1000 genomes]
rs9919793	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1037003	chr12:86610040-86798121	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1053234	chr12:86701070-86774957	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	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
5	nsv1041126	chr12:86736601-86774957	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	diseases
6	nsv1051494	chr12:86736601-86776021	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4842483	PPFIA2	cis	cerebellum	SCAN
rs4842483	SNORA20	trans	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86761400-86769600	Weak transcription	Fetal Heart	heart
2	chr12:86764000-86764800	Flanking Active TSS	HUVEC	blood vessel

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