Variant report

Variant	rs6583662
Chromosome Location	chr10:91586116-91586117
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91585659..91588157-chr10:92199771..92201481,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1125326	0.91[EUR][1000 genomes]
rs12240414	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12244597	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12252414	0.92[EUR][1000 genomes]
rs12263026	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12265484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12763878	0.81[EUR][1000 genomes]
rs12763984	0.91[EUR][1000 genomes]
rs12766364	0.91[EUR][1000 genomes]
rs12773439	0.91[EUR][1000 genomes]
rs12775585	0.83[EUR][1000 genomes]
rs1326198	0.89[EUR][1000 genomes]
rs1326199	0.92[EUR][1000 genomes]
rs17127746	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17127968	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17128049	0.84[EUR][1000 genomes]
rs17385594	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2148276	0.91[EUR][1000 genomes]
rs2181946	0.83[EUR][1000 genomes]
rs2182397	0.91[EUR][1000 genomes]
rs34395627	0.91[EUR][1000 genomes]
rs34407717	0.91[EUR][1000 genomes]
rs34498741	0.91[EUR][1000 genomes]
rs34498979	0.91[EUR][1000 genomes]
rs34548995	0.92[EUR][1000 genomes]
rs34833458	0.91[EUR][1000 genomes]
rs35305443	0.91[EUR][1000 genomes]
rs35494197	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35495765	0.91[EUR][1000 genomes]
rs35557724	0.91[EUR][1000 genomes]
rs35762262	0.81[EUR][1000 genomes]
rs35768372	0.91[EUR][1000 genomes]
rs36067049	0.91[EUR][1000 genomes]
rs36075457	0.91[EUR][1000 genomes]
rs3740040	0.92[EUR][1000 genomes]
rs3740042	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3802651	0.92[EUR][1000 genomes]
rs55932503	0.92[EUR][1000 genomes]
rs55977662	0.91[EUR][1000 genomes]
rs56246606	0.91[EUR][1000 genomes]
rs56318801	0.91[EUR][1000 genomes]
rs57160906	0.91[EUR][1000 genomes]
rs57529292	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57585079	0.91[EUR][1000 genomes]
rs57603165	0.91[EUR][1000 genomes]
rs58250931	0.85[EUR][1000 genomes]
rs58929000	0.91[EUR][1000 genomes]
rs58933281	0.84[EUR][1000 genomes]
rs60634654	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60925336	0.91[EUR][1000 genomes]
rs61128077	0.91[EUR][1000 genomes]
rs61303211	0.91[EUR][1000 genomes]
rs61646033	0.82[EUR][1000 genomes]
rs61869791	0.82[EUR][1000 genomes]
rs61869800	0.82[EUR][1000 genomes]
rs68147789	0.93[EUR][1000 genomes]
rs7076194	0.93[EUR][1000 genomes]
rs7076219	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7083051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7475158	0.91[EUR][1000 genomes]
rs7895272	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7895530	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7895851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7895863	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7899499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7908739	0.92[EUR][1000 genomes]
rs7918018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046241	chr10:91478562-91614437	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv869080	chr10:91498641-91712834	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1036581	chr10:91526705-91691536	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1043571	chr10:91568555-92036154	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv551874	chr10:91570211-92036154	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6583662	RP11-248C1.3	cis	Adipose Subcutaneous	GTEx
rs6583662	LINC00865	cis	lung	GTEx
rs6583662	KIF20B	cis	cerebellum	SCAN
rs6583662	LINC00865	cis	Esophagus Muscularis	GTEx
rs6583662	LINC00865	cis	Nerve Tibial	GTEx
rs6583662	LINC00865	cis	Artery Aorta	GTEx
rs6583662	RP11-248C1.3	cis	Artery Tibial	GTEx
rs6583662	LINC00865	cis	Thyroid	GTEx
rs6583662	RP11-248C1.3	cis	Thyroid	GTEx
rs6583662	RP11-248C1.3	cis	Nerve Tibial	GTEx
rs6583662	LINC00865	cis	Artery Tibial	GTEx
rs6583662	RP11-248C1.3	cis	Esophagus Muscularis	GTEx
rs6583662	LIPJ	cis	parietal	SCAN
rs6583662	LINC00865	cis	Adipose Subcutaneous	GTEx

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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