Variant report

Variant	rs58123872
Chromosome Location	chr2:53104452-53104453
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53103066..53106486-chr2:53106611..53109718,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1011229	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10496009	1.00[EUR][1000 genomes]
rs12470339	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12471375	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12477060	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1376565	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1377958	0.92[EUR][1000 genomes]
rs1454403	1.00[EUR][1000 genomes]
rs1549748	1.00[EUR][1000 genomes]
rs17043593	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17043603	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17043607	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17043719	0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17043720	0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17043721	0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17043766	1.00[EUR][1000 genomes]
rs17043814	1.00[EUR][1000 genomes]
rs17043816	1.00[EUR][1000 genomes]
rs1868904	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839750	1.00[EUR][1000 genomes]
rs34669934	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3770388	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41403348	0.91[ASN][1000 genomes]
rs41523148	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4524156	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4671948	0.85[EUR][1000 genomes]
rs4672031	0.94[ASN][1000 genomes]
rs56066502	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56122338	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56361754	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57955203	0.85[EUR][1000 genomes]
rs59711835	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60553623	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73933669	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7575309	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7577236	0.85[EUR][1000 genomes]
rs7602150	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs965442	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998380	chr2:52891706-53222155	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	esv2763631	chr2:52910862-53169629	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006244	chr2:52958322-53169617	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1005813	chr2:52959769-53114865	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1010978	chr2:52959769-53249951	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1014068	chr2:52960353-53169617	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv520722	chr2:53039770-53421015	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1010237	chr2:53072736-53116413	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	nsv581978	chr2:53091691-53227749	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	nsv874136	chr2:53101066-53218774	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53094400-53108600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:53102600-53108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:53104200-53104600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:53104400-53107200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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