Variant report

Variant	rs7899499
Chromosome Location	chr10:91588001-91588002
allele	C/T
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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIF20B-2	chr10:91586955-91590598	NONHSAT015541
2	lnc-KIF20B-2	chr10:91586955-91590598	NONHSAT015542

Extended variants
information (count: 72 )
Associated
traits (count: 15 )

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	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs12252414	0.92[EUR][1000 genomes]
rs12263026	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12265484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17127968	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[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	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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]
rs6583662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs68147789	0.93[EUR][1000 genomes]
rs7076194	0.93[EUR][1000 genomes]
rs7076219	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7083051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7475158	0.91[EUR][1000 genomes]
rs7895272	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895530	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7895851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895863	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908739	0.92[EUR][1000 genomes]
rs7918018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7899499	RP11-248C1.3	cis	Nerve Tibial	GTEx
rs7899499	LINC00865	cis	Skin Sun Exposed Lower leg	GTEx
rs7899499	LINC00865	cis	Esophagus Muscularis	GTEx
rs7899499	LINC00865	cis	Artery Aorta	GTEx
rs7899499	RP11-248C1.3	cis	Thyroid	GTEx
rs7899499	RP11-248C1.3	cis	Esophagus Muscularis	GTEx
rs7899499	LINC00865	cis	Artery Tibial	GTEx
rs7899499	LINC00865	cis	lung	GTEx
rs7899499	RP11-248C1.3	cis	lung	GTEx
rs7899499	RP11-248C1.3	cis	Artery Aorta	GTEx
rs7899499	LINC00865	cis	Adipose Subcutaneous	GTEx
rs7899499	RP11-248C1.3	cis	Artery Tibial	GTEx
rs7899499	RP11-248C1.3	cis	Adipose Subcutaneous	GTEx
rs7899499	LINC00865	cis	Nerve Tibial	GTEx
rs7899499	LINC00865	cis	Thyroid	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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