Variant report

Variant	rs11830208
Chromosome Location	chr12:86742782-86742783
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 183 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:175)

rs_ID	r²[population]
rs10506931	0.84[CEU][hapmap]
rs10506934	1.00[CEU][hapmap]
rs10506935	0.85[CEU][hapmap]
rs10745407	0.83[JPT][hapmap]
rs10745408	0.83[JPT][hapmap]
rs10745416	0.84[JPT][hapmap]
rs10745419	0.84[JPT][hapmap]
rs10776955	0.83[JPT][hapmap]
rs10776961	0.84[JPT][hapmap]
rs10858408	0.83[JPT][hapmap]
rs10858412	0.84[JPT][hapmap]
rs10858415	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs11103930	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs11103983	0.84[JPT][hapmap]
rs11830448	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs12303046	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12304593	0.94[EUR][1000 genomes]
rs12305255	0.92[CEU][hapmap]
rs12306280	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12306726	0.91[CEU][hapmap]
rs12307279	1.00[CEU][hapmap]
rs12309874	0.92[ASN][1000 genomes]
rs12315617	1.00[CEU][hapmap]
rs12316480	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12319410	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs12319593	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs12579580	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs12581639	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs12581912	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs12582690	0.83[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12582767	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs1389296	0.84[CEU][hapmap]
rs1552840	0.83[CEU][hapmap]
rs1628799	0.88[JPT][hapmap]
rs1698787	0.83[JPT][hapmap]
rs17013664	0.88[JPT][hapmap]
rs17013683	0.88[JPT][hapmap]
rs17013858	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs17013981	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs17014005	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs17014008	0.88[JPT][hapmap]
rs17014009	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs17014020	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs17014026	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs17040806	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs17285589	0.91[CEU][hapmap]
rs17288772	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs17288800	0.92[CEU][hapmap]
rs17289052	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17289087	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs17289115	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs17289150	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs17289178	1.00[CEU][hapmap]
rs17289646	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs17289938	0.85[CEU][hapmap]
rs17357233	0.84[CEU][hapmap]
rs17357259	0.80[CEU][hapmap]
rs17357469	0.83[CEU][hapmap]
rs17359446	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17367374	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17367869	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17367946	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs17369073	0.85[CEU][hapmap]
rs1922743	0.92[CEU][hapmap]
rs1986602	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1986603	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs1994863	0.86[JPT][hapmap]
rs2141927	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs2220782	0.83[JPT][hapmap]
rs2405793	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2405794	0.85[CEU][hapmap]
rs2405795	0.85[CEU][hapmap]
rs2405925	0.84[JPT][hapmap]
rs2405928	0.84[JPT][hapmap]
rs2405929	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs2405930	0.89[JPT][hapmap]
rs2405931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2406115	0.84[JPT][hapmap]
rs2406116	0.83[JPT][hapmap]
rs2406118	0.83[JPT][hapmap]
rs2406122	0.83[JPT][hapmap]
rs2406123	0.83[JPT][hapmap]
rs2406127	0.83[JPT][hapmap]
rs2406128	0.82[JPT][hapmap]
rs2406158	0.85[CEU][hapmap];0.93[TSI][hapmap]
rs2406160	0.94[JPT][hapmap]
rs2452807	0.83[JPT][hapmap]
rs2465144	0.83[JPT][hapmap]
rs2471560	0.83[JPT][hapmap]
rs2471568	0.83[JPT][hapmap]
rs2471569	0.83[JPT][hapmap]
rs2897240	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs2897274	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs2897275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2897277	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2897278	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2897280	0.84[JPT][hapmap]
rs4370997	0.94[JPT][hapmap]
rs4488269	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4526834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4628748	0.84[JPT][hapmap]
rs4636736	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4842454	0.89[CEU][hapmap]
rs4842468	1.00[CEU][hapmap]
rs4842487	1.00[CEU][hapmap]
rs4842557	0.91[CEU][hapmap]
rs4842558	0.81[CEU][hapmap]
rs4842640	1.00[CEU][hapmap]
rs5022626	0.80[CEU][hapmap]
rs55649116	0.94[EUR][1000 genomes]
rs55733909	0.94[EUR][1000 genomes]
rs55820226	0.98[EUR][1000 genomes]
rs55956857	0.88[EUR][1000 genomes]
rs56293486	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57002922	0.91[ASN][1000 genomes]
rs60436792	0.94[EUR][1000 genomes]
rs60555693	0.92[ASN][1000 genomes]
rs61014498	0.91[ASN][1000 genomes]
rs61133374	0.98[EUR][1000 genomes]
rs61949047	0.85[EUR][1000 genomes]
rs61949048	0.88[EUR][1000 genomes]
rs61949049	0.88[EUR][1000 genomes]
rs61949475	0.98[EUR][1000 genomes]
rs61949482	0.96[EUR][1000 genomes]
rs61949483	0.90[EUR][1000 genomes]
rs61950663	0.88[EUR][1000 genomes]
rs61950665	0.88[EUR][1000 genomes]
rs61950667	0.88[EUR][1000 genomes]
rs61950671	0.88[EUR][1000 genomes]
rs61950674	0.88[EUR][1000 genomes]
rs61950706	0.93[EUR][1000 genomes]
rs61950711	0.98[EUR][1000 genomes]
rs61950712	0.98[EUR][1000 genomes]
rs61950713	0.97[EUR][1000 genomes]
rs61950714	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61950746	0.98[EUR][1000 genomes]
rs61950747	0.98[EUR][1000 genomes]
rs61950748	0.98[EUR][1000 genomes]
rs61950749	0.98[EUR][1000 genomes]
rs6538023	0.85[JPT][hapmap]
rs6538024	0.93[JPT][hapmap]
rs6538025	0.83[JPT][hapmap]
rs6538029	0.83[JPT][hapmap]
rs6538033	0.84[JPT][hapmap]
rs7135177	0.82[JPT][hapmap]
rs7299319	0.84[JPT][hapmap]
rs7301129	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs767898	0.94[EUR][1000 genomes]
rs7953196	0.82[JPT][hapmap]
rs7961251	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs7964553	0.83[JPT][hapmap]
rs7973773	0.83[JPT][hapmap]
rs7980126	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs839104	0.83[JPT][hapmap]
rs839148	0.83[JPT][hapmap]
rs839149	0.83[JPT][hapmap]
rs839151	0.83[JPT][hapmap]
rs839152	0.86[JPT][hapmap]
rs839153	0.83[JPT][hapmap]
rs839156	0.83[JPT][hapmap]
rs839157	0.83[JPT][hapmap]
rs839158	0.82[JPT][hapmap]
rs839159	0.83[JPT][hapmap]
rs839162	0.88[JPT][hapmap]
rs839165	0.83[JPT][hapmap]
rs839166	0.83[JPT][hapmap]
rs839168	0.83[JPT][hapmap]
rs839170	0.82[JPT][hapmap]
rs839171	0.83[JPT][hapmap]
rs844434	0.82[JPT][hapmap]
rs844435	0.83[JPT][hapmap]
rs863392	0.82[JPT][hapmap]
rs863395	0.83[JPT][hapmap]
rs865138	0.83[JPT][hapmap]
rs865721	0.83[JPT][hapmap]

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	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
5	nsv1053234	chr12:86701070-86774957	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	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
7	nsv1041126	chr12:86736601-86774957	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	diseases
8	nsv1051494	chr12:86736601-86776021	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11830208	SLC6A15	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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