Variant report

Variant	rs55728546
Chromosome Location	chr5:52665592-52665593
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	chr5:52646929..52648945-chr5:52664247..52665920,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11958087	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1363966	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1423548	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17243137	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1862606	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1862607	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1978463	0.86[EUR][1000 genomes]
rs1978464	0.86[EUR][1000 genomes]
rs1978465	0.86[EUR][1000 genomes]
rs55658556	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56005425	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56144882	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56170221	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56179015	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56261541	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56266381	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56276302	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56392803	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56405129	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62357785	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357786	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357787	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357795	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357821	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357822	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357823	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357824	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357826	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357828	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62357835	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62359262	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62359266	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62359268	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62359276	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62359282	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62359311	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv830297	chr5:52492494-52707758	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv508356	chr5:52646168-52703120	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52662600-52674200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:52663200-52666000	Enhancers	NHDF-Ad	bronchial
3	chr5:52663400-52665800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:52663400-52665800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:52663800-52665800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:52663800-52665800	Enhancers	HMEC	breast
7	chr5:52664800-52669400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:52665000-52667000	Weak transcription	NHEK	skin
9	chr5:52665000-52669000	Weak transcription	HUVEC	blood vessel
10	chr5:52665000-52669200	Weak transcription	Osteobl	bone
11	chr5:52665000-52669800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:52665000-52674200	Weak transcription	NH-A	brain
13	chr5:52665200-52672200	Weak transcription	NHLF	lung
14	chr5:52665400-52674200	Weak transcription	Hela-S3	cervix

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