Variant report

Variant	rs1997246
Chromosome Location	chr2:62867347-62867348
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	chr2:62866392..62868630-chr2:62870444..62872522,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10172216	0.88[AFR][1000 genomes]
rs10177638	0.81[AFR][1000 genomes]
rs10208675	0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs1038570	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11125934	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11678011	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13398408	0.89[CHD][hapmap]
rs1386400	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs1534418	0.86[LWK][hapmap];0.82[MKK][hapmap];0.94[YRI][hapmap]
rs1534419	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1843778	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872789	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2200562	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2204655	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2421712	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2931488	1.00[JPT][hapmap]
rs2969300	1.00[JPT][hapmap]
rs34503992	0.89[CHD][hapmap]
rs36009942	0.89[CHD][hapmap]
rs360786	0.89[CHD][hapmap]
rs360793	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs360794	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs360795	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs360796	1.00[JPT][hapmap]
rs360798	0.89[CHD][hapmap]
rs360802	0.89[CHD][hapmap]
rs360805	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs360806	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4273204	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4671446	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545968	0.94[YRI][hapmap]
rs6705835	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6759928	0.81[ASN][1000 genomes]
rs6760804	0.90[CEU][hapmap];0.90[JPT][hapmap]
rs7587936	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs974345	0.85[AFR][1000 genomes]
rs9752159	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62832200-62868800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:62861400-62869000	Weak transcription	Ovary	ovary

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