Variant report

Variant	rs6679539
Chromosome Location	chr1:85479457-85479458
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10443172	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs10782537	0.81[GIH][hapmap]
rs11161512	0.82[MEX][hapmap]
rs11588160	0.91[EUR][1000 genomes]
rs12024977	0.92[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap]
rs12028736	0.85[ASN][1000 genomes]
rs12030730	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs12030837	0.91[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs12037219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12041012	0.84[ASN][1000 genomes]
rs12042018	0.91[EUR][1000 genomes]
rs12042160	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12042845	0.91[EUR][1000 genomes]
rs12042910	0.94[EUR][1000 genomes]
rs12045710	0.94[EUR][1000 genomes]
rs1371140	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs1371141	0.83[EUR][1000 genomes]
rs1371142	0.82[EUR][1000 genomes]
rs1371143	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs1837329	0.94[ASN][1000 genomes]
rs1853776	0.91[EUR][1000 genomes]
rs2028304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2039814	1.00[YRI][hapmap]
rs2083283	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes]
rs2083284	0.91[EUR][1000 genomes]
rs2304641	1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2840050	0.92[CEU][hapmap];0.93[CHB][hapmap]
rs4907122	1.00[YRI][hapmap]
rs55721024	0.94[EUR][1000 genomes]
rs614194	0.80[YRI][hapmap]
rs61768850	0.94[EUR][1000 genomes]
rs61768852	0.94[EUR][1000 genomes]
rs61768853	0.94[EUR][1000 genomes]
rs61768854	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61770879	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6576740	0.90[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs6576743	0.90[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs6665436	0.92[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap]
rs6672362	0.92[CEU][hapmap];0.84[CHB][hapmap];0.94[EUR][1000 genomes]
rs6680422	0.94[EUR][1000 genomes]
rs6688354	1.00[CEU][hapmap];0.85[ASN][1000 genomes]
rs6690464	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs6690583	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs6699356	0.86[EUR][1000 genomes]
rs6699956	0.94[EUR][1000 genomes]
rs6700723	0.84[ASN][1000 genomes]
rs7519717	0.93[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs7522239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540706	1.00[CEU][hapmap]
rs7547224	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs7547317	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs893618	0.84[ASN][1000 genomes]
rs893620	0.91[EUR][1000 genomes]
rs898036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription 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
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv3418404	chr1:85479398-85479694	Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85478800-85483800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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