Variant report

Variant	rs2660173
Chromosome Location	chr10:55733691-55733692
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10740557	0.87[CEU][hapmap]
rs10740558	0.87[CEU][hapmap]
rs10763020	0.87[CEU][hapmap]
rs10763021	0.87[CEU][hapmap]
rs10763022	0.86[CEU][hapmap]
rs10763024	0.87[CEU][hapmap]
rs10763025	0.87[CEU][hapmap]
rs10763027	0.87[CEU][hapmap]
rs10763038	1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs10825138	0.87[CEU][hapmap]
rs10825156	0.87[CEU][hapmap]
rs10825157	0.87[CEU][hapmap]
rs10825185	0.92[CEU][hapmap]
rs11003893	0.87[CEU][hapmap]
rs11003894	1.00[JPT][hapmap]
rs11003918	0.91[CEU][hapmap]
rs11003919	0.87[CEU][hapmap]
rs11003969	0.91[CEU][hapmap]
rs1900421	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1900422	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1900423	0.87[CEU][hapmap]
rs1900425	0.85[GIH][hapmap]
rs1900427	0.85[GIH][hapmap]
rs1900444	0.91[CEU][hapmap]
rs1900446	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1900450	0.87[CEU][hapmap]
rs1900451	0.87[CEU][hapmap]
rs1900453	0.87[CEU][hapmap];0.82[TSI][hapmap]
rs1900458	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1900459	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1911420	0.91[CEU][hapmap]
rs1911427	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1911429	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs1911430	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs2121525	0.92[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2135718	0.91[CEU][hapmap]
rs2135723	0.87[CEU][hapmap]
rs2166620	0.83[EUR][1000 genomes]
rs2166621	0.83[EUR][1000 genomes]
rs2166628	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2174716	0.88[CEU][hapmap]
rs2384327	0.81[EUR][1000 genomes]
rs2384328	0.87[CEU][hapmap]
rs2384340	0.87[CEU][hapmap];0.81[MEX][hapmap]
rs2384343	0.92[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2446600	0.83[CEU][hapmap]
rs2446608	1.00[CEU][hapmap]
rs2446609	1.00[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2456699	0.96[CEU][hapmap]
rs2456701	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2593103	0.87[CEU][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs2593105	0.87[CEU][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs2593106	0.87[CEU][hapmap]
rs2593107	0.86[CEU][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2593120	0.87[CEU][hapmap]
rs2593122	0.87[CEU][hapmap];0.82[TSI][hapmap]
rs2593123	0.87[CEU][hapmap]
rs2593129	0.91[CEU][hapmap]
rs2593131	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2593133	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs2593135	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs2593136	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs2610823	0.87[CEU][hapmap]
rs2610837	0.82[CEU][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs2610891	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs2610893	0.95[CEU][hapmap]
rs2610899	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2610902	0.95[CEU][hapmap];0.83[YRI][hapmap]
rs2610906	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2610908	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs2610909	0.96[CEU][hapmap]
rs2610910	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2610912	0.87[CEU][hapmap]
rs2610919	0.87[CEU][hapmap]
rs2660172	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs2660178	0.83[CEU][hapmap]
rs2660183	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs2660184	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs2660186	0.96[CEU][hapmap];0.91[YRI][hapmap]
rs2660188	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2660190	1.00[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2660192	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2660197	0.96[CEU][hapmap]
rs2921912	0.87[CEU][hapmap]
rs2921924	0.87[CEU][hapmap]
rs2921925	0.87[CEU][hapmap];0.81[MEX][hapmap]
rs2921926	0.87[CEU][hapmap]
rs2926391	0.87[CEU][hapmap]
rs2926397	0.87[CEU][hapmap];0.82[TSI][hapmap]
rs2926404	0.83[CEU][hapmap]
rs2926408	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2926410	0.83[CEU][hapmap]
rs4478892	0.85[GIH][hapmap]
rs4478893	0.85[GIH][hapmap]
rs4935485	0.88[CEU][hapmap]
rs4935487	0.84[CEU][hapmap]
rs5003374	0.88[CEU][hapmap]
rs6481043	0.87[CEU][hapmap]
rs6481045	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7069577	0.88[CEU][hapmap]
rs7095839	0.87[CEU][hapmap]
rs7097365	0.87[GIH][hapmap]
rs7476991	0.96[CEU][hapmap]
rs7893789	0.87[CEU][hapmap]
rs7896419	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7896432	0.88[EUR][1000 genomes]
rs7896582	0.90[EUR][1000 genomes]
rs7899816	0.87[EUR][1000 genomes]
rs7904289	0.87[CEU][hapmap]
rs7910658	0.87[CEU][hapmap]
rs7911482	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7912992	0.83[EUR][1000 genomes]
rs7915856	0.83[EUR][1000 genomes]
rs7920872	0.88[CEU][hapmap]

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	esv1842975	chr10:55378668-55736655	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv949692	chr10:55502542-55893206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv895429	chr10:55564355-55736655	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv895430	chr10:55645953-55736655	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1052939	chr10:55654719-55769239	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv869303	chr10:55714219-55857931	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2660173	DKK1	cis	parietal	SCAN
rs2660173	PCDH15	cis	parietal	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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