Variant report

Variant	rs28673554
Chromosome Location	chr4:125204570-125204571
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	chr4:125202856..125205436-chr4:125209965..125212090,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10001440	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10003154	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010227	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10012163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10012961	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10013370	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10019486	1.00[AMR][1000 genomes]
rs10019630	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027794	1.00[AMR][1000 genomes]
rs10031876	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10050287	1.00[AMR][1000 genomes]
rs10213036	1.00[AMR][1000 genomes]
rs10222808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10470920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10471024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13434913	1.00[AMR][1000 genomes]
rs28375948	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28416609	1.00[AMR][1000 genomes]
rs28430925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28445476	1.00[AMR][1000 genomes]
rs28473649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28475344	1.00[AMR][1000 genomes]
rs28524723	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28555360	1.00[AMR][1000 genomes]
rs28582977	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28595372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28623216	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28690319	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28691138	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28750428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28750489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28794011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28827314	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28841956	1.00[AMR][1000 genomes]
rs28847327	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28848204	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28873723	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9307539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9307540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9992929	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9997645	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv868977	chr4:124841128-125550637	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv432624	chr4:125013395-125367740	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv998024	chr4:125019384-125380876	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv537241	chr4:125019384-125380876	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015049	chr4:125037090-125393067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv517857	chr4:125147414-125248489	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv879880	chr4:125174817-125494547	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv3443643	chr4:125189396-125206061	Enhancers Active TSS Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125200000-125205400	Weak transcription	Fetal Heart	heart
2	chr4:125203200-125204600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:125204200-125204600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:125204200-125211200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:125204400-125205200	Weak transcription	HMEC	breast

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