Variant report

Variant	rs13404419
Chromosome Location	chr2:53721499-53721500
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53720586..53722714-chr2:53727046..53728819,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10165742	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10167973	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10174983	0.81[AMR][1000 genomes]
rs10183446	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10183776	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10191277	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10204173	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10204330	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10204468	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12472781	0.87[EUR][1000 genomes]
rs13394011	0.81[AMR][1000 genomes]
rs13394939	0.81[AMR][1000 genomes]
rs13404175	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13404343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416219	0.82[AMR][1000 genomes]
rs1472238	0.81[AMR][1000 genomes]
rs1565796	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17268033	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4671411	0.81[AMR][1000 genomes]
rs4672452	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4672453	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4672456	0.82[AMR][1000 genomes]
rs4672464	0.81[AMR][1000 genomes]
rs6742054	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67822265	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7560576	0.81[AMR][1000 genomes]
rs7571640	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7577504	0.81[AMR][1000 genomes]
rs7586356	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7586411	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7586468	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7586738	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7596693	0.81[AMR][1000 genomes]
rs7596877	0.81[AMR][1000 genomes]
rs7597009	0.81[AMR][1000 genomes]
rs7599710	0.81[AMR][1000 genomes]
rs7604056	0.81[AMR][1000 genomes]
rs7607091	0.81[AMR][1000 genomes]
rs961241	0.82[AMR][1000 genomes];0.85[EUR][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	nsv1002145	chr2:53387912-53832213	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv535718	chr2:53387912-53832213	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv997401	chr2:53515629-53863347	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv999571	chr2:53690538-53775723	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1012754	chr2:53690538-53785037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv457873	chr2:53701324-53785037	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv582009	chr2:53701324-53785037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53718000-53724200	Weak transcription	Aorta	Aorta
2	chr2:53718200-53725200	Weak transcription	Brain Anterior Caudate	brain
3	chr2:53718200-53737600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:53718600-53723600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:53718600-53724200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:53718800-53724600	Weak transcription	Hela-S3	cervix
7	chr2:53720600-53723400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:53721200-53721600	Enhancers	Left Ventricle	heart
9	chr2:53721200-53721600	Enhancers	Pancreas	Pancrea

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