Variant report

Variant	rs17289115
Chromosome Location	chr12:86745185-86745186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10506931	0.84[CEU][hapmap]
rs10506934	1.00[CEU][hapmap]
rs10506935	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs11830208	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs12304593	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12305255	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs12306280	0.92[EUR][1000 genomes]
rs12306726	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs12307279	1.00[CEU][hapmap]
rs12315617	1.00[CEU][hapmap]
rs12316480	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12582690	0.94[EUR][1000 genomes]
rs1389296	0.84[CEU][hapmap]
rs1552840	0.83[CEU][hapmap]
rs17285589	0.91[CEU][hapmap]
rs17288772	0.92[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17288800	0.92[CEU][hapmap]
rs17289052	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17289087	1.00[CEU][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs17289150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs17289178	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17289646	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][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];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17367374	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17367869	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17367946	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs17369073	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs1922743	0.92[CEU][hapmap];0.90[AMR][1000 genomes]
rs1994863	1.00[YRI][hapmap]
rs2405794	0.85[CEU][hapmap]
rs2405795	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs2406157	0.90[AMR][1000 genomes]
rs2406158	0.85[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes]
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	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55733909	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55820226	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55870715	0.90[AMR][1000 genomes]
rs55904324	0.90[AMR][1000 genomes]
rs55956857	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56293486	0.96[EUR][1000 genomes]
rs60436792	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61133374	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61949013	0.82[AMR][1000 genomes]
rs61949037	0.82[AMR][1000 genomes]
rs61949039	0.82[AMR][1000 genomes]
rs61949045	0.84[AMR][1000 genomes]
rs61949047	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61949048	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61949049	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61949475	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61949482	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61949483	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61949532	0.90[AMR][1000 genomes]
rs61949533	0.90[AMR][1000 genomes]
rs61949558	0.90[AMR][1000 genomes]
rs61949559	0.87[AMR][1000 genomes]
rs61950663	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61950665	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61950667	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61950671	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61950674	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61950706	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61950711	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61950712	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61950713	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61950714	0.98[EUR][1000 genomes]
rs61950746	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61950747	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61950748	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61950749	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61950760	0.87[AMR][1000 genomes]
rs61950761	0.90[AMR][1000 genomes]
rs61950762	0.90[AMR][1000 genomes]
rs61950763	0.90[AMR][1000 genomes]
rs61950764	0.90[AMR][1000 genomes]
rs61950771	0.90[AMR][1000 genomes]
rs61950775	0.90[AMR][1000 genomes]
rs61950780	0.90[AMR][1000 genomes]
rs61950781	0.85[AMR][1000 genomes]
rs73189394	0.87[AMR][1000 genomes]
rs73189397	0.90[AMR][1000 genomes]
rs73191472	0.90[AMR][1000 genomes]
rs73191477	0.90[AMR][1000 genomes]
rs73191482	0.90[AMR][1000 genomes]
rs73191485	0.90[AMR][1000 genomes]
rs73191486	0.90[AMR][1000 genomes]
rs767898	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9705580	0.82[AMR][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	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
rs17289115	SLC6A15	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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