Variant report

Variant	rs2406615
Chromosome Location	chr5:52513535-52513536
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10043264	0.81[EUR][1000 genomes]
rs10070123	0.81[EUR][1000 genomes]
rs10071518	0.81[EUR][1000 genomes]
rs10940294	0.81[EUR][1000 genomes]
rs10940296	0.81[EUR][1000 genomes]
rs10940308	0.83[EUR][1000 genomes]
rs11740027	0.81[EUR][1000 genomes]
rs11743062	0.81[EUR][1000 genomes]
rs11745943	0.81[EUR][1000 genomes]
rs11955319	0.81[EUR][1000 genomes]
rs12517334	0.86[EUR][1000 genomes]
rs12520159	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12521034	0.81[EUR][1000 genomes]
rs1318732	0.86[EUR][1000 genomes]
rs1374052	0.80[EUR][1000 genomes]
rs1374053	0.80[EUR][1000 genomes]
rs1374054	0.80[EUR][1000 genomes]
rs1445985	0.80[EUR][1000 genomes]
rs1445992	0.81[EUR][1000 genomes]
rs16881069	0.81[EUR][1000 genomes]
rs16881173	0.86[EUR][1000 genomes]
rs16881189	0.83[EUR][1000 genomes]
rs17241927	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17242584	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1813600	0.86[EUR][1000 genomes]
rs1838736	0.81[EUR][1000 genomes]
rs1960785	0.84[EUR][1000 genomes]
rs1960786	0.85[EUR][1000 genomes]
rs2112876	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2406617	0.86[EUR][1000 genomes]
rs2897474	0.81[EUR][1000 genomes]
rs2897475	0.81[EUR][1000 genomes]
rs34277022	0.81[EUR][1000 genomes]
rs4106003	0.81[EUR][1000 genomes]
rs56197881	0.81[EUR][1000 genomes]
rs56296560	0.83[EUR][1000 genomes]
rs56686182	0.81[EUR][1000 genomes]
rs56909170	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58049370	0.80[EUR][1000 genomes]
rs62357405	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62357407	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62357423	0.81[EUR][1000 genomes]
rs62357424	0.81[EUR][1000 genomes]
rs62357427	0.81[EUR][1000 genomes]
rs62357430	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62357442	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6414820	0.81[EUR][1000 genomes]
rs6450112	0.81[EUR][1000 genomes]
rs6860071	0.81[EUR][1000 genomes]
rs6866517	0.80[EUR][1000 genomes]
rs6873915	0.81[EUR][1000 genomes]
rs6875198	0.81[EUR][1000 genomes]
rs6885965	0.80[EUR][1000 genomes]
rs6892815	0.80[EUR][1000 genomes]
rs6895908	0.80[EUR][1000 genomes]
rs6896916	0.81[EUR][1000 genomes]
rs6897066	0.81[EUR][1000 genomes]
rs6897187	0.81[EUR][1000 genomes]
rs6897912	0.81[EUR][1000 genomes]
rs72762377	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7705986	0.81[EUR][1000 genomes]
rs7707949	0.81[EUR][1000 genomes]
rs7710423	0.81[EUR][1000 genomes]
rs7711335	0.81[EUR][1000 genomes]
rs7724504	0.81[EUR][1000 genomes]
rs7724705	0.81[EUR][1000 genomes]
rs7725098	0.81[EUR][1000 genomes]
rs7725139	0.81[EUR][1000 genomes]
rs7725380	0.80[EUR][1000 genomes]
rs7725467	0.81[EUR][1000 genomes]
rs7726216	0.81[EUR][1000 genomes]
rs7726834	0.81[EUR][1000 genomes]
rs9292012	0.81[EUR][1000 genomes]
rs9292013	0.81[EUR][1000 genomes]
rs9918202	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv515913	chr5:52492677-52545841	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv522454	chr5:52492677-52571758	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv880833	chr5:52502168-52544231	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52509600-52540000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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