Variant report

Variant	rs2406115
Chromosome Location	chr12:86694130-86694131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 161 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10431399	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs10745407	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10745408	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10745416	0.94[JPT][hapmap]
rs10776955	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10776957	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10776959	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10776961	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10776966	0.96[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs10776968	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10776969	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs10776971	0.83[CEU][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.92[TSI][hapmap]
rs10776977	0.94[JPT][hapmap]
rs10858408	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10858409	0.82[ASN][1000 genomes]
rs10858412	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10858415	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs10858419	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10858425	0.84[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs10858427	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs10858428	0.84[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11103912	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11103930	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs11830208	0.84[JPT][hapmap]
rs12303046	0.80[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12306280	0.98[ASN][1000 genomes]
rs12309874	0.81[ASN][1000 genomes]
rs12317113	0.84[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs12578669	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs12582690	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1463749	0.96[CEU][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs1493415	0.95[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1493416	0.95[EUR][1000 genomes]
rs1532262	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs1552839	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs1602848	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1602850	0.95[EUR][1000 genomes]
rs1689340	0.91[CEU][hapmap]
rs1689357	0.89[EUR][1000 genomes]
rs1698787	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs1922742	0.94[JPT][hapmap]
rs1922749	0.87[CEU][hapmap];0.95[JPT][hapmap]
rs1948448	0.96[EUR][1000 genomes]
rs1955399	0.89[JPT][hapmap]
rs2091818	0.80[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap]
rs2131565	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2220782	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2405923	0.87[CEU][hapmap]
rs2405925	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2405928	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2405930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405931	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2405933	0.86[EUR][1000 genomes]
rs2406116	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2406117	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2406118	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2406119	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2406121	0.81[ASN][1000 genomes]
rs2406122	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2406123	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2406127	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2406128	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2452806	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs2452807	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2452811	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2452815	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2465143	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.96[EUR][1000 genomes]
rs2465144	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs2465146	0.95[EUR][1000 genomes]
rs2465147	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2465149	0.92[CEU][hapmap]
rs2471560	0.89[ASW][hapmap];0.92[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2471564	0.92[CEU][hapmap]
rs2471568	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2471569	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs2471570	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2897275	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2897277	0.80[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2897278	0.88[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2897280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4265650	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4334094	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4503614	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4526834	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4628748	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4842483	0.91[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs56293486	0.83[ASN][1000 genomes]
rs57002922	0.83[ASN][1000 genomes]
rs60555693	0.81[ASN][1000 genomes]
rs61014498	0.83[ASN][1000 genomes]
rs6538024	0.80[JPT][hapmap]
rs6538025	0.92[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap]
rs6538028	0.91[CEU][hapmap]
rs6538029	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6538031	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6538032	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6538033	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs6538042	0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs7134946	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7135177	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7135733	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7135741	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7137308	0.96[CEU][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs7139324	0.94[JPT][hapmap]
rs7299319	0.84[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs7303642	0.81[ASN][1000 genomes]
rs7303796	0.95[JPT][hapmap]
rs7310186	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7953196	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7957560	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7963659	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs7964553	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7972484	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7973773	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7977689	0.89[JPT][hapmap]
rs7980126	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs839101	0.81[EUR][1000 genomes]
rs839104	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs839105	0.88[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap]
rs839137	0.83[CHB][hapmap]
rs839148	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs839149	0.89[JPT][hapmap]
rs839150	0.87[JPT][hapmap]
rs839151	0.89[JPT][hapmap]
rs839152	0.87[JPT][hapmap]
rs839153	0.89[JPT][hapmap]
rs839154	0.83[JPT][hapmap]
rs839156	0.89[JPT][hapmap]
rs839157	0.96[CEU][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs839158	0.89[JPT][hapmap]
rs839159	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs839163	0.84[EUR][1000 genomes]
rs839164	0.84[EUR][1000 genomes]
rs839165	0.92[CEU][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs839166	0.89[JPT][hapmap]
rs839168	0.96[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs839170	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs839171	0.96[CEU][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs839191	0.82[CEU][hapmap]
rs844434	0.89[JPT][hapmap]
rs844435	0.96[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap]
rs863392	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs863394	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs863395	0.96[CEU][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs865138	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs865721	0.89[JPT][hapmap]
rs9919783	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919793	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
8	nsv1045386	chr12:86616015-86733418	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv541565	chr12:86616015-86733418	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv1843214	chr12:86673989-86703959	Weak transcription Enhancers ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
11	esv1850061	chr12:86673989-86703959	ZNF genes & repeats Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
12	nsv802	chr12:86683758-86723684	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3378364	chr12:86690521-86695319	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2406115	SNORA20	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86690600-86698200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:86693800-86694600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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