Variant report

Variant	rs839104
Chromosome Location	chr12:86608721-86608722
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 148 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10745407	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10745408	0.83[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10776955	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10776957	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10776959	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10776961	0.92[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs10776966	0.92[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs10776968	0.84[EUR][1000 genomes]
rs10776969	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs10858408	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10858412	0.89[JPT][hapmap]
rs10858415	0.83[JPT][hapmap]
rs10858419	0.87[EUR][1000 genomes]
rs10858425	0.86[GIH][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap]
rs11103930	0.83[JPT][hapmap]
rs11830208	0.83[JPT][hapmap]
rs11830448	0.83[JPT][hapmap]
rs12303046	0.83[JPT][hapmap]
rs12311449	0.86[YRI][hapmap]
rs12317113	0.86[GIH][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap]
rs12319410	0.83[JPT][hapmap]
rs12319593	0.81[JPT][hapmap]
rs12578669	0.84[JPT][hapmap]
rs12581639	0.83[JPT][hapmap]
rs12582690	0.89[JPT][hapmap]
rs1463749	0.92[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs1493415	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1493416	0.85[EUR][1000 genomes]
rs1532262	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1552839	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1602848	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1602850	0.85[EUR][1000 genomes]
rs1628799	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1689340	0.96[CEU][hapmap]
rs1689357	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1698787	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013858	0.83[JPT][hapmap]
rs17013981	0.83[JPT][hapmap]
rs1948448	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1986602	0.83[JPT][hapmap]
rs1986603	0.83[JPT][hapmap]
rs1994863	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2131565	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2220782	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2405923	0.82[CEU][hapmap]
rs2405925	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs2405928	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs2405929	0.83[JPT][hapmap]
rs2405930	0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs2405931	0.83[JPT][hapmap]
rs2406115	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2406116	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406117	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406118	0.84[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406119	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406122	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406123	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406127	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2406128	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2452806	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2452807	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2452811	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2452815	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2465143	0.92[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2465144	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2465146	0.86[EUR][1000 genomes]
rs2465147	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2465149	0.96[CEU][hapmap]
rs2471560	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2471564	0.96[CEU][hapmap]
rs2471568	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2471569	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2471570	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2897274	0.83[JPT][hapmap]
rs2897275	0.83[JPT][hapmap]
rs2897277	0.83[JPT][hapmap]
rs2897278	0.84[CEU][hapmap];0.83[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2897280	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs4265650	0.95[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4334094	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4503614	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4526834	0.83[JPT][hapmap]
rs4628748	0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4842483	0.86[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs6538023	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs6538024	0.82[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6538025	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap]
rs6538028	0.87[CEU][hapmap]
rs6538029	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6538031	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6538032	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6538033	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap]
rs7134946	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7135177	0.84[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7135733	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7135741	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7137308	0.92[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7299319	0.92[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap]
rs7310186	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7953196	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7957560	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7964553	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7972484	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7973773	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7980126	0.83[JPT][hapmap]
rs839101	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs839105	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap]
rs839118	0.83[CHB][hapmap]
rs839128	0.90[TSI][hapmap]
rs839137	0.94[CHB][hapmap]
rs839148	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs839149	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839150	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs839151	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839152	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839154	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs839156	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs839158	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839162	0.83[JPT][hapmap]
rs839163	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839164	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839165	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839166	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839171	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs839189	0.88[TSI][hapmap]
rs839191	0.86[CEU][hapmap]
rs844434	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs844435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs863392	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs863394	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs863395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs865138	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs865721	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9919783	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9919793	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv2761759	chr12:86415936-86747726	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	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1053087	chr12:86569126-86733418	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541564	chr12:86569126-86733418	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv800	chr12:86572379-86617887	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
8	esv11568	chr12:86604717-86609023	Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs839104	SNORA20	trans	cerebellum	SCAN
rs839104	PPFIA2	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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